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1. bwa bwa Public

   Forked from lh3/bwa

   Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

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2. gatk gatk Public

   Forked from broadinstitute/gatk

   Official code repository for GATK versions 4 and up

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3. samtools samtools Public

   Forked from samtools/samtools

   Tools (written in C using htslib) for manipulating next-generation sequencing data

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4. FREEC FREEC Public

   Forked from BoevaLab/FREEC

   Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data

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5. seqtk seqtk Public

   Forked from lh3/seqtk

   Toolkit for processing sequences in FASTA/Q formats

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6. sra-tools sra-tools Public

   Forked from ncbi/sra-tools

   SRA Tools

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