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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

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

metage2metabo

From annotated genomes to metabolic screening in large scale microbiotas

looper

Modular job submitter for arbitrary pipelines or commands.

bacalhau-apiclient

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

bacalhau-sdk

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

piaso-tools

Precise Integrative Analysis of Single-cell Omics.

ariba

ARIBA: Antibiotic Resistance Identification By Assembly

phigaro

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

lorax

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

runjob

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

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.

bacalhau-airflow

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

nphase

Ploidy agnostic phasing pipeline and algorithm

gmql

Python Library for data analysis based on GMQL

circlator

A tool to circularize genome assemblies

hybkit

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

iva

Iterative Virus Assembler

viralquest

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

tcga-gdc-downloader

User-friendly tool to download TCGA STAR RNA-seq counts from the GDC portal

pycrispr

Pip package for CRISPR-Cas9 screen analysis

pyrpipe

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.