bioinformatics-pipelines

Here are 8 public repositories matching this topic...

prairie-guy / parallel_zip

A Python wrapper for GNU parallel that naturally embeds shell code into Python scripts or Jupyter notebooks (no delimiter hell). Features parameter substitution, environment substitution, and cross-product generation to eliminate shell loops. Perfect for integrating Unix programs into Python environments for bioinformatics and data science.

python data-science bioinformatics parallel-computing bioinformatics-pipeline shell-scripting gnu-parallel shell-wrappers parallel-computing-toolbox jupyter-pipeline data-science-pipeline bioinformatics-pipelines shell-integration subprocess-alternative jupyter-shell notebook-integration embed-shell-commands shell-from-python jupyter-bash

Updated Jun 28, 2025
Python

ishandutta2007 / Awesome-Scientific-Workflow-Management

Sponsor

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Top Scientific Workflow Management (Opensource) 🌟 Star if you like it! 🌟

awesome-list scientific-workflows curated-list workflow-management workflow-orchestration bioinformatics-pipelines

Updated Sep 9, 2026

nermze / MOSTAR

Star

Ont-only and Hybrid Assembly, Polishing, Annotation, AMR, Plasticity, prophage tracker, & ICE detection

bioinformatics annotation taxonomy assembly bioinformatics-pipeline amr illumina oxford-nanopore bioinformatics-tool prophage bioinformatics-pipelines ice-detection

Updated Aug 20, 2026
Shell

pirl-unc / nexus

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A command-line streamliner for Nextflow bioinformatics pipelines.

nextflow bioinformatics-pipelines

Updated Aug 6, 2026
Nextflow

natlee-the-anteel / reactrv1.0

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reactrv1.0 is a modular bioinformatics pipeline that automates exploration and analysis of genes, in addition to integrating wet-lab applications

snakemake research multi-omics bioinformatics-pipelines plant-bio

Updated Aug 13, 2026
Python

mahvin92 / Seed-Aligner

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Seed Aligner is a light-weight tool that detects a common seed region across genetic sequences and reorders them to start at the same point. It standardizes FASTA inputs for Covary without performing full multiple sequence alignment.