Samtools Python Packages

pyfaidx

Efficient pythonic random access to fasta subsequences

filtersam

Tools to filter SAM/BAM files by percent identity and percent of matched sequence

amplicon-coverage-inspector

Some NGS library preps use amplicons, and it can be difficult to determine the coverage and depth of each amplicon.

bamrefine

Small program to mask positions that are likely to result in PMD artifact from a BAM file using a predefined SNP catalog

rubam

Pure-Rust BAM/VCF/BCF depth, pileup, variants & stats with Python bindings — native Linux/macOS/Windows wheels, pysam-parity, no htslib.

filtersam-tools

Tools to filter SAM/BAM files by percent identity and percent of matched sequence

plasmiduncover

Script to obtain plasmid id from WGS data using bowtie2 to map

yafax

Yet Another FASTA Index and Extraction Tool

bampy

Python implementation of htslib supporting BAM, SAM, and BGZF compression