Bioinformatics Pipeline Python Packages

piper

Python toolkit for building restartable pipelines

44K 47 9

sprocket-bio

A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).

10K 218 80

napari-vipp

VIPP — Visual Image Processing Platform: Visual image processing made approachable

3K 6 1

bystro

Natural Language Search and Analysis of High Dimensional Genomic Data

3K 49 6

piaso-tools

PIASO: Precise Integrative Analysis of Single-cell Omics

3K 16 3

hicstuff

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

2K 42 9

rnalysis

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

2K 139 22

metage2metabo

From annotated genomes to metabolic screening in large scale microbiotas

2K 77 6

viralquest

A user-friendly pipeline for viral diversity analysis and characterization.

1K 16 2

ariba

Antimicrobial Resistance Identification By Assembly

829 187 60

bacalhau-apiclient

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

822 874 105

lorax

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

758 1 2

bacalhau-sdk

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

699 874 105

molforge

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

656 2 0

looper

Modular job submitter for arbitrary pipelines or commands.

648 26 7

fulcrum-ms

Fulcrum Pipeline: extreme-scale proteomics processing engine from Seer

624 2 2

circlator

A tool to circularize genome assemblies

551 258 57

phigaro

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

550 53 15

runjob

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

539 11 4

bacalhau-airflow

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

515 874 105

nphase

Ploidy agnostic phasing pipeline and algorithm

492 51 6

splicekit

splicekit: an integrative toolkit for splicing analysis from short-read RNA-seq

349 23 4

iva

de novo virus assembler of Illumina paired reads

272 58 18

foldpipe

Bounded-memory asynchronous streaming for native PyTorch/PyG molecular-data shards, with remote prefetch from Hugging Face and Google Drive.

260 0 0