DETAILED ACTION Notice of Pre-AIA or AIA Status The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA. Status of Claims Claims 1- 20 pending and examined on the merits. Priority The instant application filed on 8/22/2022 claims the benefit of priority to U.S. Provisional Patent Application No. 63/245,639 filed on 9/17/2021. Thus, the effective filing date of the claims is 9/17/2021. The applicant is reminded that amendments to the claims and specification must comply with 35 U.S.C. § 120 and 37 C.F.R. § 1.121 to maintain priority to an earlier-filed application. Claim amendments may impact the effective filing date if new subject matter is introduced that lacks support in the originally filed disclosure. If an amendment adds limitations that were not adequately described in the parent application, the claim may no longer be entitled to the priority date of the earlier filing. Information Disclosure Statement The information disclosure statement (IDS) filed on 3/2/2023 has been entered and considered. A signed copy of the corresponding 1449 form has been included with this Office action. Claim Rejections - 35 USC § 112 The following is a quotation of 35 U.S.C. 112(b): (b ) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention. The following is a quotation of 35 U.S.C. 112 (pre-AIA), second paragraph: The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the appl icant regards as his invention. Claim s 1-20 rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. Claims 1, 12, and 17 recite "determine base-call-error rates at which nucleotide-base calls generated by a sequencing pipeline differ from reference bases in a reference genome". It is not clear how "base-call-error rates" are being determined from the "nucleotide-base calls [reads] generated by a sequencing pipeline". Assuming these reads are aligned to the reference bases in the reference genome, what are the criteria for an error to be called? Additionally, what sample is being used for generating the reads? Can it be any nucleic acid sample, or a sample from the organism associated with the reference genome? To further prosecution, the limitation is interpreted as "determine base-call-error rates for data produced by a sequencing run of a nucleic acid sample associated with a reference genome at which nucleotide-base calls generated by a sequencing pipeline differ from reference bases in the reference genome, wherein the base-call-error rates comprise a single nucleotide polymorphism (SNP), an insertion or a deletion (indel), or base call that is part of a structural variant" (instant specification para.0032-33 and para.0106), and the broadest reasonable interpretation of "differ from reference bases in the reference genome" is any difference (even a single instance of a mismatched nucleotide). Claims 1, 12, and 17 recite "detect one or more base-call-error patterns from the base-call-error rates grouped according to base-call-error types". It is not clear what kind of "base-call-error types" (groups) are meant to be used for detecting a pattern from/among. In other words, what error types are being assigned (transversions, transitions, adjacent nucleotides, single- or multi-nucleotide insertion/deletion, or others including machinery, reagent, chemistry, or software related types of base-call-errors)? Additionally, the quoted limitation attempts to claim a process without setting forth any steps involved in the process. Without knowing the types of base-call-errors one would not be able to generate groups of them for pattern detection, and the steps for how patterns are detected are not claimed. Therefore, the claim is indefinite because it merely recites a use without any active, positive steps delimiting how this use is actually practiced similar to the findings in Ex parte Erlich , 3 USPQ2d 1011 (Bd. Pat. App. & Inter. 1986). To further prosecution, the "base-call-error types" are interpreted as described in para.0056-58 of the instant specification and Figure 2 of the drawings (para.0058 " FiG. 2 illustrates a 3-dimensional chart representing a base-call-error pattern for a sequencing pipeline. The 3-dimensional chart represents base-call-error rates grouped by both base-call-error type and neighboring nucleotide bases"), and the process of detecting base-call-error patterns from base-call-error rate groups based on types is interpreted as described in the instant specification para.0059-60 "FIG. 2 also illustrates the variation-source-identification system 106 performing an act 206 of identifying one or more sample base-call-error patterns for one or more sample sequencing runs. Generally, the variation-source-identification system 106 identifies sample-base-call-error patterns that fall within a threshold similarity with the base- call-error pattern. In particular, the variation-source-identification system 106 generates sample base-call-error patterns using sample sequencing runs. The variation-source-identification system 106 further utilizes a statistical method and manufacturing data associated with the sample sequencing runs to determine failure sources of variation within the sequencing runs. For example, and as illustrated in FIG. 2, the variation-source-identification system 106 determines that sample base-call-error pattern 212 is within a threshold similarity of base-call-error pattern 210. [0060] As part of the series of acts 200 illustrated in FIG. 2, the variation-source-identification system 106 performs an act 208 of determining a failure source. Based on a correlation between the base-call-error pattern and the sample base-call-error pattern, the variation-source- identification system 106 determines a failure source for the base-call-error type corresponding to the sequencing pipeline. In some embodiments, the variation-source-identification system 106 utilizes a statistical model to determine contribution metrics indicating probabilities of sequencing- pipeline materials contributing to base-call errors from the sequencing pipeline. The variation- source-identification system 106 can further determine the failure source for the base-call-error types based on the contribution metrics". Claim 11 recites "truncating the manufacturing identification data". The claim does not make clear the details of how the truncation of manufacturing identification data is to be performed, or what identification data is to be truncated (are they only numbers, combination of numbers and letters, brand names, device names, etc.). To further prosecution the limitation is interpreted as disclosed on para.0113 "For example, manufacturing data can comprise a lot number or a date of production or release associated with a reagent, part, or software version" and in Figure 6A. Claim 19 recites "normalizing a confusion matrix comprising base-call-error data based on a total of correct nucleotide-base calls for a specific type of nucleotide-base call and one or more of cycle, time, or nucleotide read for a base-call error". It is not clear what is meant by normalizing by "a total of correct nucleotide-base calls [] and one or more [] nucleotide read". In order words, what data from the "nucleotide read" is being used with the "total of correct nucleotide-base calls" for normalizing the confusion matrix (minimum/maximum/average/ etc read length of the reads containing the error, etc.). Likewise, it is not clear how cycle or time would be incorporated into the normalization of the confusion matrix, not to mention how those variables would differ from one another given that the cycle number is generally dependent on time (granted there could have been an unexpected pause between cycles, or some other unforeseen issue). Additionally, the quoted limitation attempts to claim a process without setting forth any steps involved in the process. Without knowing the type of data and method for utilizing said data, one would not be able to normalize the confusion matrix and the steps for normalization are not claimed. Therefore, the claim is indefinite because it merely recites a use without any active, positive steps delimiting how this use is actually practiced similar to the findings in Ex parte Erlich , 3 USPQ2d 1011 (Bd. Pat. App. & Inter. 1986). The disclosure does not illuminate these matters beyond what is claimed here, therefore, claim 19 is interpreted as not further limiting claim 17. All other claims depend from independent claims 1, 12, or 17, and therefore are also rejected as being indefinite under 35 USC 112(b). The following is a quotation of the first paragraph of 35 U.S.C. 112(a): (a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention. The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112: The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention. Claim 19 rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention. Regarding claim 19 , the written description of the instant specification does not explicitly disclose a means to "normalizing a confusion matrix comprising base-call-error data based on a total of correct nucleotide-base calls for a specific type of nucleotide-base call and one or more of cycle, time, or nucleotide read for a base-call error". The type of data and steps for utilizing said data are not disclosed in the instant specification, and one would not be able to practice the limitation as claimed. Therefore, claim 19 is interpreted as not further limiting claim 17. The following is a quotation of 35 U.S.C. 112(d): (d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers. The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph: Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers. Claim 2 rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Claim 2 rejected as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends. Claim 2 recites "determine the base-call-error rates by determining nucleotide-specific error rates at which nucleotide-base calls generated by the sequencing pipeline differ from the reference bases", which does not further limit claim 1 because claim 1 recites "determine base-call-error rates at which nucleotide-base calls generated by a sequencing pipeline differ from reference bases in a reference genome". There is no distinction made between a "nucleotide-specific error rate" and a "base-call-error rate" in the instant specification, and the disclosure even conflates the two occasionally (e.g. para.0046 "the sequencing system 104 can detect base- call errors within a sequencing run by comparing nucleotide-base calls for a reference genome against known reference bases for the reference genome", para.0054 "the variation-source-identification system 106 determines error rates at which nucleotide-base calls generated by the sequencing pipeline differ from the known reference bases of the reference genome", etc.). Both claims are determining a "base-call-error rate", but claim 2 adds "by determining nucleotide-specific error rates" which is interpreted here as being redundant to the limitation of claim 1. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements. Claim Rejections - 35 USC § 101 35 U.S.C. 101 reads as follows: Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title. Claims 1- 1 0 and 12-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of a mental process, a mathematical concept, organizing human activity, or a law of nature or natural phenomenon without significantly more. In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea: Claim s 1 , 12, and 17 : “ determine base-call-error rates at which nucleotide-base calls generated by a sequencing pipeline differ from reference bases in a reference genome ” provides a comparison (determining differing bases calls involves assessing similarities or differences between items) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea. “ detect one or more base-call-error patterns from the base-call-error rates grouped according to base-call-error types ” provides for recognizing patterns (detecting base-call-error patterns involves identifying trends or structures in data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea. “ identify one or more sample base-call-error patterns for one or more sample sequencing runs that utilize one or more sequencing pipelines corresponding to the sequencing pipeline ” provides for recognizing patterns (identifying base-call-error patterns between sequencing runs involves identifying trends or structures in data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea. “ determine a failure source for a base-call-error type corresponding to the sequencing pipeline ” provides an evaluation (determining a failure source based on a correlation involves making determinations based on data or experience) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea. Claim s 3 and 18 : “ determine the base-call-error rates grouped according to the base-call-error types and different neighboring nucleotide bases respectively flanking incorrect nucleotide-base calls ” provides an evaluation (determining groups based on base-call-error type and flanking nucleotide-case calls involves making determinations based on data or experience) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea. “ detect the one or more base-call-error patterns from the base-call-error rates grouped according to the base-call-error types and the different neighboring nucleotide bases ” provides for recognizing patterns (detecting base-call-error patterns involves identifying trends or structures in data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea. Claims 4 and 13: “ determining contribution metrics indicating contributions of sequencing-pipeline materials to base-call errors from the sequencing pipeline ” provides an evaluation (determining contribution metrics involves making determinations based on data or experience) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea. “ determining the failure source for the base-call-error type based on the contribution metrics ” provides an evaluation (determining the failure source involves making determinations based on data or experience) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea. Claim 5: “ determining assignable cause variations for the sequencing-pipeline materials contributing to the base-call errors from the sequencing pipeline ” provides an evaluation (determining assignable cause variations involves making determinations based on data or experience) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea. Claim 7: “ identifying a consumable product, a part of a sequencing machine, a software application or feature, or a part of a nucleotide-sample slide as a contributing factor to a sequencing variation in the sequencing pipeline ” provides an evaluation (identifying a feature as a failure source contributing factor involves making determinations based on data or experience) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea. Claims 8 and 16: “ determine the base-call-error rates by utilizing a confusion matrix ” (claim 8) and “ normalizing a confusion matrix comprising base-call-error data based on a total of correct nucleotide-base calls for a specific type of nucleotide-base call ” (claim 16) provides a mathematical calculation (utilizing or normalizing a confusion matrix involves mathematical calculations) that is considered a mathematical concept, which is an abstract idea. Claim s 9 and 15 : “ categorizing sets of sample sequencing runs from sample sequencing runs that utilize similar manufacturing materials based on manufacturing identification data ” provides classifying and organizing information (categorizing sequencing runs based on manufacturing materials involves sorting or structuring data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea. “ detecting different sample base-call-error patterns for the sets of sample sequencing runs ” provides for recognizing patterns (detecting base-call-error patterns involves identifying trends or structures in data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea. “ identifying the one or more sample base-call-error patterns from among the different sample base-call-error patterns for the sets of sample sequencing runs based on the correlation between the one or more base-call-error patterns and the one or more sample base-call-error patterns ” provides for recognizing patterns (identifying base-call-error patterns between sequencing runs involves identifying trends or structures in data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea. Claim 10: “ determining sample nucleotide-specific error rates at which the sample nucleotide-base calls differ from the reference bases ” provides a comparison (determining differing bases calls involves assessing similarities or differences between items) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea. “ grouping the sample nucleotide-specific error rates according to the base-call-error types and different neighboring nucleotide bases respectively flanking incorrect nucleotide-base calls ” provides an evaluation (determining groups based on base-call-error type and flanking nucleotide-case calls involves making determinations based on data or experience) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea. Claim 20: “ utilizing a variance components model to determine percentages of assignable cause variations for sequencing-pipeline materials contributing to base-call errors of the base-call-error type ” provides a mathematical calculation (determining percentages involves mathematical calculations) that is considered a mathematical concept, which is an abstract idea. These recitations are similar to the concepts of collecting information, analyzing it, and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014)) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind or are mathematical relationships. Therefore, these limitations fall under the “Mental process” and “Mathematical concepts” group ings of abstract ideas. Additionally, while claims 1-1 6 recite performing some aspects of the analysis on “ A system comprising: at least one processor; and a non-transitory computer readable medium comprising instructions ” (claim 1) and “ A non-transitory computer readable medium comprising instructions ” (claim 12) , there are no additional limitations that indicate that this requires anything other than carrying out the recited mental processes or mathematical concepts in a generic computer environment. Merely reciting that a mental process is being performed in a generic computer environment does not preclude the steps from being performed practically in the human mind or with pen and paper as claimed. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then it falls within the “Mental processes” grouping of abstract ideas. As such, claims 1-10 and 12-20 recite an abstract idea (Step 2A, Prong 1: YES). Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). The judicial exceptions listed above are not integrated into a practical application because the claims do not recite an additional element or elements that reflects an improvement to technology. Specifically, the claims recite the following additional elements: Claim 1: “ A system comprising: at least one processor; and a non-transitory computer readable medium comprising instructions ” provides insignificant extra-solution activities (running instructions on generic computer components) that do not serve to integrate the judicial exceptions into a practical application. Claim 6 : “ provide, for display on a computing device associated with the sequencing pipeline, a notification indicating the failure source ” provides insignificant extra-solution activities (displaying a notification is a post-solution activity involving data manipulation steps) that do not serve to integrate the judicial exceptions into a practical application. Claim 12 : “ A non-transitory computer readable medium comprising instructions ” provides insignificant extra-solution activities (running instructions on generic computer components) that do not serve to integrate the judicial exceptions into a practical application. The steps for displaying data are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application because they are post-solution activities involving data manipulation steps (see MPEP 2106.04(d)(2)). Furthermore, the limitations regarding implementing program instructions do not indicate that they require anything other than mere instructions to implement the abstract idea in a generic way or in a generic computing environment. As such, this limitation equates to mere instructions to implement the abstract idea on a generic computer that the courts have stated does not render an abstract idea eligible in Alice Corp., 573 U .S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. Therefore, claims 1-10 and 12-20 are directed to an abstract idea (Step 2A, Prong 2: NO). Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application, or equate to mere instructions to apply the recited exception in a generic way or in a generic computing environment. As discussed above, there are no additional elements to indicate that the claimed “ A system comprising: at least one processor; and a non-transitory computer readable medium comprising instructions” (claim 1) and “A non-transitory computer readable medium comprising instructions” (claim 12) requires anything other than generic computer components in order to carry out the recited abstract idea in the claims. Claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. MPEP 2106.05(f) discloses that mere instructions to apply the judicial exception cannot provide an inventive concept to the claims. Additionally, the limitations for displaying data are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application. Furthermore, no inventive concept is claimed by these limitations as they are well-understood, routine, and conventional: para.0003 “High … reference.” Ling et al. (US-20010044129) reinforces the assertion that no inventive concept is claimed by these limitations as they are well-understood, routine, and conventional . The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B: No ). As such, claims 1-10 and 12-20 are not patent eligible. Claim Rejections - 35 USC § 103 In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis ( i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status. The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action: A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made. Claims 1, 3-7, 9-10, 12-15, and 17-18 rejected under 35 U.S.C. 103 as being unpatentable over Blachly et al. ( WO-2021126896 ). Regarding claim s 1 , 3-5, 7, 9-10, 12-15, and 17-18 , Blachly teaches : determine base-call-error rates for data produced by a sequencing run of a nucleic acid sample associated with a reference genome at which nucleotide-base calls generated by a sequencing pipeline differ from reference bases in the reference genome, wherein the base-call-error rates comprise a single nucleotide polymorphism (SNP), an insertion or a deletion (indel), or base call that is part of a structural variant (as interpreted above) ; and detect one or more base-call-error patterns from the base-call-error rates grouped according to base-call-error types (as interpreted above, which incorporates the limitations of claims 3- 5, 7, 9-10, 13-15, and 18) ( Para.0066 "The error profiles are determined through systematic experimentation, by determining how often a given NGS instrument (type or model) and combination of conditions correctly detected alleles, and the frequencies of correct and incorrect base calls and the related Q score distributions of these correct and incorrect calls at different genomic loci and in different genomic contexts for different combinations of kits/ basecallers , etc " , para.0095 "It was annotated whether the expected sequence was wildtype (matching the reference), had a mismatch (nucleotide substitution), or an insertion or deletion of nucleotides" ; and p ara.0098 "To further improve accuracy, the process can be repeated separately for mismatches, insertions, and deletions, to identify an optimal scaling for each type of error. Furthermore, mismatches can also be further broken down to represent each potential 3- nucleotide codon that may be incorrectly called, to account for non-random patterns in the error profile" ). Blachly also teaches based on the one or more base-call-error patterns, identify one or more sample base-call-error patterns for one or more sample sequencing runs that utilize one or more sequencing pipelines corresponding to the sequencing pipeline ( Para.0098 "To further improve accuracy, the process can be repeated separately for mismatches, insertions, and deletions, to identify an optimal scaling for each type of error. Furthermore, mismatches can also be further broken down to represent each potential 3- nucleotide codon that may be incorrectly called, to account for non-random patterns in the error profile" ). Blachly also teaches based on a correlation between the one or more base-call-error patterns and the one or more sample base-call-error patterns, determine a failure source for a base-call-error type corresponding to the sequencing pipeline ( Para.0014 "Additionally, each set of locus-specific error profiles for the base is associated with a different combination of a sequencing device model, a basecaller algorithm, a kit type, and/or a flowcell or chemistry type" ). It is recognized that the citations and evidence provided above are derived from potentially different embodiments of a single reference. Nevertheless, it would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains to employ combinations and sub-combinations of these complementary embodiments, because Blachly et al. explicitly motivates doing so at least in para.0066, 0075, and 0104 including "Through experimentation and statistical analysis, locus-specific error profiles can be determined for the given allele and combination of Q score threshold/library kit/input nucleic acid type/ flowcell / basecaller , etc " and otherwise motivating experimentation and optimization. Additionally, doing so merely combines prior art elements according to known methods to yield predictable results. Regarding claim 6 , Blachly teach es the methods of Claims 1 on which this claim depends/these claims depend, respectively. Blachly also teaches provid ing , for display on a computing device associated with the sequencing pipeline, a notification indicating the failure source ( Para.0072 "The report may be displayed on the display device 102 and/or printed on the printer 103" ). Claim 8 rejected under 35 U.S.C. 103 as being unpatentable over Blachly et al. ( WO-2021126896 ) as applied to claims 1, 3-7, 9-10, 12-15, and 17-18 above, and further in view of Laehnemann et al. ( Briefings in bioinformatics 17.1 (2016): 154-179 ). Blachly et al. is applied to claims 1, 3-7, 9-10, 12-15, and 17-18 . Regarding claim 8 , Blachly teach es the method of Claim 1 on which this claim depends/these claims depend. Blachly does not explicitly teach determine the base-call-error rates by utilizing a confusion matrix . However, Laehnemann teaches determine the base-call-error rates by utilizing a confusion matrix ( Page 19 col 2 second to last paragraph "Therefore, an approach used by several tools (Supplementary Note S5) is to employ an empirically determined base confusion matrix that gives the probability of every possible base substitution separately instead of assuming a uniform substitution probability (i.e. a matrix with 4 by 4 substitution probabilities)" ). Therefore, it would have been obvious to one of ordinary skill in the art as of the effective filing date of the claimed invention to modify the methods of Blachly as taught by Laehnemann in order to characterize base calling errors common to high-throughput sequencing platforms (page 1 abstract "Characterizing the errors generated by common high-throughput sequencing platforms and telling true genetic variation from technical artefacts are two interdependent steps, essential to many analyses such as single nucleotide variant calling, haplotype inference, sequence assembly and evolutionary studies"). One skilled in the art would have a reasonable expectation of success because both methods are concerned with determining base call errors. Claim 16 rejected under 35 U.S.C. 103 as being unpatentable over Blachly et al. ( WO-2021126896 ) as applied to claims 1, 3-7, 9-10, 12-15, and 17-18 above , and further in view of Laehnemann et al. ( Briefings in bioinformatics 17.1 (2016): 154-179 ) and Landgrebe et al. ( IEEE transactions on pattern analysis and machine intelligence 30.5 (2008): 810-822 ). Blachly et al. is applied to claims 1, 3-7, 9-10, 12-15, and 17-18 . Regarding claim 16 , Blachly teaches the method of Claim 1 on which this claim depends/these claims depend. Blachly does not explicitly teach determin ing the base-call-error rates by utilizing a confusion matrix and normalizing a confusion matrix comprising base-call-error data based on a total of correct nucleotide-base calls for a specific type of nucleotide-base call . However, Laehnemann teaches determin ing the base-call-error rates by utilizing a confusion matrix ( Page 19 col 2 second to last paragraph "Therefore, an approach used by several tools (Supplementary Note S5) is to employ an empirically determined base confusion matrix that gives the probability of every possible base substitution separately instead of assuming a uniform substitution probability (i.e. a matrix with 4 by 4 substitution probabilities)" ). However, Landgrebe teaches normalizing a confusion matrix ( Page 12 Figure 4 " Normalised confusion matrix for the Digits dataset example, with unit weighting on the left, and a perturbation of φ7 on the right" demonstrates normalization of a multiclass confusion matrix, and it would have been obvious to normalize the error rates of the confusion matrix of Laehnemann with the normalization method on Landgrebe in order to make a proper comparison between failure sources because converting raw counts into proportions or percentages makes it easier to interpret imbalanced datasets ). Therefore, it would have been obvious to one of ordinary skill in the art as of the effective filing date of the claimed invention to modify the methods of Blachly as taught by Laehnemann in order to characterize base calling errors common to high-throughput sequencing platforms (page 1 abstract "Characterizing the errors generated by common high-throughput sequencing platforms and telling true genetic variation from technical artefacts are two interdependent steps, essential to many analyses such as single nucleotide variant calling, haplotype inference, sequence assembly and evolutionary studies"). One skilled in the art would have a reasonable expectation of success because both methods are concerned with determining base call errors. Therefore, it would have been obvious to one of ordinary skill in the art as of the effective filing date of the claimed invention to modify the methods of Blachly as taught by Landgrebe in order to confer ROC analysis to the present pattern recognition problem (page 2 last paragraph "Extension to the multiclass case is attractive since it would confer the benefits of ROC analysis to many more problems in pattern recognition"). One skilled in the art would have a reasonable expectation of success because both methods are concerned with evaluating a confusion matrix of classifications. Claim 20 rejected under 35 U.S.C. 103 as being unpatentable over Blachly et al. ( WO-2021126896 ) as applied to claims 1, 3-7, 9-10, 12-15, and 17-18 above , and further in view of Tourlousse et al. ( Microbiome 9.1 (Apr. 2021): 95 ). Blachly et al. is applied to claims 1, 3-7, 9-10, 12-15, and 17-18 . Regarding claim 20 , Blachly teaches the method of Claim 1 on which this claim depends/these claims depend. Blachly does not explicitly teach determining the correlation between the one or more base-call-error patterns and the one or more sample base-call-error patterns by utilizing a variance components model to determine percentages of assignable cause variations for sequencing-pipeline materials contributing to base-call errors of the base-call-error type . However, Tourlousse teaches determining the correlation between the one or more base-call-error patterns and the one or more sample base-call-error patterns by utilizing a variance components model to determine percentages of assignable cause variations for sequencing-pipeline materials contributing to base-call errors of the base-call-error type ( Page 8 col 2 last paragraph "We next performed decomposition of variance components by analysis of variance (ANOVA) based on Aitchison distances and summarized variability in terms of qmCV values estimated from resulting metric variance components (see Supplementary Methods). With respect to sequencing library construction, both intermediate precision and interlaboratory reproducibility were high" ). Therefore, it would have been obvious to one of ordinary skill in the art as of the effective filing date of the claimed invention to modify the methods of Blachly as taught by Tourlousse in order to summarize and compare variability of base call errors across protocols (page 5 col 1 paragraph 2 "Finally, base call error rates were largely comparable across protocols, although positional effects were observed in some cases"). One skilled in the art would have a reasonable expectation of success because both methods are concerned with comparing variability of base call error patterns. Conclusion No claims are allowed. Claim 11 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims. In this case, claims 1 and 9 are rejected under 35 USC 101 as being directed to an abstract idea, however claim 11 contains the additional element of "truncating the manufacturing identification data" (the manufacturing data being interpreted as described in section "Claim Rejections - 35 USC 112", above), which integrates said judicial exceptions into patent eligible subject matter because truncating manufacturing identification data from sequencing runs in order to group them via thresholding of shared data is not routine or conventional (Step 2B: Yes) . The closest prior art is considered to be Blachly , as discussed above relating to the rejection of claims 1 and 9 under 35 USC 103. As discussed above, Blachly teaches grouping base-call-error rates by various types and associating those with a sequencing device model, a basecaller algorithm, a kit type, and/or a flowcell or chemistry type. However, there is no teaching or motivation present to truncate manufacturing identifiers in order to group them for base-call-error rate correlation. Inquiries Any inquiry concerning this communication or earlier communications from the examiner should be directed to FILLIN "Examiner name" \* MERGEFORMAT Robert A. Player whose telephone number is FILLIN "Phone number" \* MERGEFORMAT 571-272-6350 . The examiner can normally be reached FILLIN "Work Schedule?" \* MERGEFORMAT Mon-Fri, 8am-5pm . Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice. If attemp ts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Larry D . Riggs can be reached at 571-270-3062. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. /R.A.P./ Examiner, Art Unit 1686 /LARRY D RIGGS II/ Supervisory Patent Examiner, Art Unit 1686