Bam Python Packages

sequali

Fast sequencing data quality metrics

turbo-picard

Picard-compatible Rust tools for faster SAM/BAM/CRAM, VCF, duplicate-marking and sequencing-QC workflows.

compas-model

A universal model datastructure for design, analysis, fabrication, and construction

fuc

Frequently used commands in bioinformatics

pymasc

Python implementation to calc mappability-sensitive cross-correlation for fragment length estimation and quality control for ChIP-Seq.

vafator

Annotate variants in a VCF file with technical annotations from one or more BAMs

chimeralm

A language model enables accurate structural variant detection in whole-genome amplified long-read sequencing

htslurp

slurp noodles-htsget streams into python

semantiseq

Semantic comparison for BAM/CRAM and VCF/BCF files, independent of record order, compression, and provenance metadata.

rubam

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

bioartifact

Lightweight, agent-friendly inspection and contract validation for bioinformatics artifacts.

biolic

A fast, modular, streaming bioinformatics toolkit in Rust for FASTQ/FASTA/BAM — a platform that grows through modules, with strong long-read support.

fast5seek

Subset of fast5 files contained in a fastq, BAM, or SAM file.

bampy

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

gendiff

Semantic comparison for BAM/CRAM and VCF/BCF files, independent of record order, compression, and provenance metadata.