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• BamBam
  ;InterSnp: takes 1 or more BAM files and writes out a ".snp" file with a summary of all polymorphic loci
  3 KB (456 words) - 18:00, 12 August 2022
• ART
  ...tion sequencing data analysis, including read alignment, de novo assembly, SNP and structure variation discovery. ART was used as a primary tool for the s
  3 KB (440 words) - 21:10, 6 December 2019
• Gmap
  Fast and SNP-tolerant detection of complex variants and splicing in short reads
  3 KB (450 words) - 17:11, 15 August 2022
• Phyluce
  * Alignment and SNP calling using UCE or other types of raw-read data.
  4 KB (517 words) - 18:23, 21 August 2022
• SHAPEIT4
  ...a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and high coverage sequencing data. The version 4 is a refactored and
  5 KB (617 words) - 19:22, 14 December 2022

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