Samtools Python Packages

pyfaidx

Efficient pythonic random access to fasta subsequences

rubam

Pure-Rust BAM/CRAM depth, pileup and stats — fast, multi-threaded, Windows-native. Originally forked from rustbam.

filtersam

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

filtersam-tools

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

amplicon-coverage-inspector

Visualization of coverage for amplicon sequencing

bamrefine

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

bampy

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

yafax

Yet Another FASTA Index and Extraction Tool

plasmiduncover

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