Ngs Python Packages

pysam

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.

peppy

Project metadata manager for biological sample metadata in Python

galaxy-util

Data intensive science for everyone.

galaxy-tool-util

Data intensive science for everyone.

arda-mapper

High-throughput mapping and domain partitioning of antigen receptor sequences

galaxy-tool-util-models

Data intensive science for everyone.

cooler

A cool place to store your Hi-C

barcode

NGS barcode design and validation.

pybgzf

Streaming BGZF compression with on-the-fly tabix and CSI indexing

deeptools

Tools to process and analyze deep sequencing data.

bedspec

An HTS-specs compliant BED toolkit

oxbow

Oxbow makes genomic data ready for high-performance analytics.

galaxy-objectstore

Data intensive science for everyone.

galaxy-job-metrics

Data intensive science for everyone.

pairtools

Extract 3D contacts (.pairs) from sequencing alignments

strkit

A short tandem repeat (STR) genotyping and analysis toolkit for long reads

cutseq

✂️ Trim sequencing adapters from NGS data automatically

turbo-picard

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

galaxy-containers

Data intensive science for everyone.

s4-clarity

A modern Python library for BaseSpace Clarity LIMS.

sequana

Sequana: a set of Snakemake NGS pipelines

galaxy-data

Data intensive science for everyone.

galaxy-app

Data intensive science for everyone.

galaxy-job-execution

Data intensive science for everyone.