Bioinformatics Pipeline Python Packages

piper

Python toolkit for building restartable pipelines

polars-pf

PFrames - Python Polars extensions

bacalhau-sdk

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

hicstuff

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

bacalhau-apiclient

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

rnalysis

Analyze your RNA sequencing data without writing a single line of code

molforge

A forge for protein workflows. One Python script, every tool in your stack.

metage2metabo

From annotated genomes to metabolic screening in large scale microbiotas

ariba

Antimicrobial Resistance Identification By Assembly

lorax

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

looper

Modular job submitter for arbitrary pipelines or commands.

piaso-tools

PIASO: Precise Integrative Analysis of Single-cell Omics

bacalhau-airflow

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

nphase

nPhase is a command line ploidy agnostic phasing pipeline and algorithm which phases samples of any ploidy with sequence alignment of long and short read data to a reference sequence.

bioartifact

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

phigaro

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

runjob

No description available

fulcrum-ms

Fulcrum Pipeline: extreme-scale proteomics processing engine from Seer

hybkit

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

circlator

A tool to circularize genome assemblies

gmql

Python Library for data analysis based on GMQL

ilus

ilus: A handy tools for generating WGS/WES analysis pipeline.

iva

Iterative Virus Assembler

viralquest

A bioinformatics tool for viral genome analysis and characterization.