Bioinformatics Pipeline Python Packages

piper

Python toolkit for building restartable pipelines

polars-pf

PFrames - Python Polars extensions

hicstuff

Simple library/pipeline to generate and handle Hi-C data.

rnalysis

RNAlysis is an analysis software for RNA sequencing data. RNAlysis can help to filter, visualize, explore, analyze, and share your data.

metage2metabo

Automatic reconstruction of draft metabolic networks with Pathway Tools and graph-based metabolic analysis

bacalhau-sdk

Compute over Data framework for public, transparent, and optionally verifiable computation using IPFS & Filecoin.

bacalhau-apiclient

Community-driven, simple, yet powerful framework for fast, cost-effective distributed Compute over Data.

looper

Modular job submitter for arbitrary pipelines or commands.

ariba

ARIBA: Antibiotic Resistance Identification By Assembly

lorax

a web server that "speaks for the (phylogenetic) trees"

bacalhau-airflow

An Apache Airflow provider for Bacalhau.

ilus

A lightweight and handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis by using GATK and Sentieon. 一个基于 GATK 和 Sentieon 的简易且全面的 WGS/WES 分析流程生成器.

phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages

piaso-tools

Precise Integrative Analysis of Single-cell Omics.

nphase

Ploidy agnostic phasing pipeline and algorithm

circlator

A tool to circularize genome assemblies

runjob

runjob is a program for managing a group of related jobs running on a compute cluster

fulcrum-ms

Extreme-scale search pipeline from Seer

gmql

Python Library for data analysis based on GMQL

hybkit

Toolkit for analysis of ".hyb" format nucleotide sequence data from chimeric RNA experiments.

iva

de novo virus assembler of Illumina paired reads

viralquest

A bioinformatics tool for viral genome analysis and characterization.

tcga-gdc-downloader

Download and annotate TCGA RNA-seq counts from the GDC portal

pyrpipe

pyrpipe