m analysis
- <a href="http://www.htslib.org/">Samtools</a> including tools for converting fastq to BAM files while mapping genes to the genome, duplicate read marking, and sorting reads
- <a href="https://broadinstitute.github.io/picard/">Picard2</a> including tools to covert fastq to SAM files, filter files, create indices, mark read duplicates, sort files, and merge files
- <a href="https://gatk.broadinstitute.org/hc/en-us">GATK</a> is a comprehensive set of tools from the Broad Institute for analyzing ma