Samtools Python Packages

pyfaidx

Efficient pythonic random access to fasta subsequences

bamrefine

A small program to mask positions that could result in a PMD artifact from a BAM file using a predefined SNP catalog

filtersam

('Tools to filter sam o bam files by percent identity or 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.

yafax

Yet Another FASTA Index and Extraction Tool

plasmiduncover

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

bampy

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