Automate common sam & bam conversions
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tools for adding mutations to existing .bam files, used for testing mutation callers
SAMStat displays various properties of next-generation sequencing reads stored in SAM/BAM format.
A versatile pairwise aligner for genomic and spliced nucleotide sequences
Mummer alignment tool
Tools (written in C using htslib) for manipulating next-generation sequencing data
Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
