mutinack | Mutation detection program

mutinack is a Java library. mutinack has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

"mutinack" is a program that detects mutations genome-wide with an error rate estimated to be as low as ~10-10, using illumina paired end sequencing of minute amounts of starting material prepared following the sip-hava-seq protocol — as described in an accompanying manuscript [1] (see [2] for the original report of the duplex sequencing idea). mutinack can report detailed statistics on mutations and top/bottom strand disagreements over any genome region defined in a custom bed file. while mutinack was primarily designed with dna-seq in mind, it can accessorily be used to collapse rna-seq reads to only keep one set of reads per molecule in a cdna library, which minimizes noise when quantifying gene expression (see e.g. [3-4]). mutinack is a java program that comes with all dependencies pre-packaged in a single mutinack.jar file. the only runtime requirement is a java >= 8 runtime (and gnu make and perl with module file::grep for functional tests), and mutinack should thus run on any platform that has such a runtime (freebsd, mac os x, and linux have been tested with openjdk 1.8 or 1.9 early access build 161). running under java 9 requires a few module-related tweaks; see branch java9 of the repository. the