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The Top 23 Python Bioinformatics Pipeline Open Source Projects

Open source projects categorized as Python Bioinformatics Pipeline
Categories > Bioinformatics Pipeline
Pysradb ⭐ 269
Package for fetching metadata and downloading data from SRA/ENA/GEO
dependent packages 7total releases 38most recent commit 7 months agopypi pysradb} Downloads
Circlator ⭐ 193
A tool to circularize genome assemblies
total releases 33most recent commit 8 months ago
Atac_dnase_pipelines ⭐ 135
ATAC-seq and DNase-seq processing pipeline
most recent commit 5 years ago
Ariba ⭐ 135
Antimicrobial Resistance Identification By Assembly
dependent packages 1total releases 54most recent commit a year agopypi ariba} Downloads
Gubbins ⭐ 133
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
most recent commit 5 months ago
Seq2science ⭐ 132
Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.
most recent commit 5 months ago
Toga ⭐ 120
TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.
most recent commit 3 months ago
Methylpy ⭐ 116
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
most recent commit a year ago
Rnalysis ⭐ 114
RNA sequencing analysis software
total releases 43most recent commit 4 months ago
Open Cravat ⭐ 98
A modular annotation tool for genomic variants
most recent commit 6 months ago
Ilus ⭐ 89
A handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis. 一个简易且全面的 WGS/WES 分析流程生成器.
total releases 13most recent commit 4 months ago
Altanalyze ⭐ 72
AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.
most recent commit 2 years ago
Snakecharm ⭐ 58
Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.
most recent commit 5 months ago
Chitin ⭐ 56
chitin: an awful shell for awful bioinformaticians
most recent commit 4 years ago
R2g ⭐ 49
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
dependent packages 1total releases 6most recent commit 3 years agopypi r2g} Downloads
Finder ⭐ 44
A fully automated gene annotator from RNA-Seq expression data
most recent commit 10 months ago
Mtoolbox ⭐ 44
A bioinformatics pipeline to analyze mtDNA from NGS data
most recent commit 4 years ago
Pypiper ⭐ 42
Python toolkit for building restartable pipelines
dependent packages 3total releases 22most recent commit 4 months agopypi piper} Downloads
Nphase ⭐ 39
Ploidy agnostic phasing pipeline and algorithm
total releases 27most recent commit 4 months ago
Iva ⭐ 37
de novo virus assembler of Illumina paired reads
total releases 16most recent commit 3 years ago
Oliver ⭐ 36
An opinionated Cromwell orchestration manager.
total releases 27most recent commit a year ago
Lsf ⭐ 29
Snakemake profile for running jobs on an LSF cluster
most recent commit 8 months ago
Bioqueue ⭐ 28
A novel pipeline framework to accelerate bioinformatics analysis
most recent commit a year ago
The 5 Most Depended On Python Bioinformatics Pipeline Open Source Projects
Pysradb ⭐ 269
Package for fetching metadata and downloading data from SRA/ENA/GEO
dependent packages 7total releases 38latest release September 17, 2023most recent commit 7 months agopypi pysradb} Downloads
Pypiper ⭐ 42
Python toolkit for building restartable pipelines
dependent packages 3total releases 22latest release November 15, 2023most recent commit 4 months agopypi piper} Downloads
Runjob ⭐ 9
runjob is a program for managing a group of related jobs running on a compute cluster
dependent packages 2total releases 39latest release November 01, 2023most recent commit 3 months agopypi runjob} Downloads
Ariba ⭐ 135
Antimicrobial Resistance Identification By Assembly
dependent packages 1total releases 54latest release September 07, 2020most recent commit a year agopypi ariba} Downloads
R2g ⭐ 49
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
dependent packages 1total releases 6latest release November 23, 2020most recent commit 3 years agopypi r2g} Downloads
The 10 Latest Releases In Python Bioinformatics Pipeline Open Source Projects
Rnalysis ⭐ 114
RNA sequencing analysis software
total releases 43latest release November 22, 2023most recent commit 4 months ago
Pypiper ⭐ 42
Python toolkit for building restartable pipelines
dependent packages 3total releases 22latest release November 15, 2023most recent commit 4 months agopypi piper} Downloads
Runjob ⭐ 9
runjob is a program for managing a group of related jobs running on a compute cluster
dependent packages 2total releases 39latest release November 01, 2023most recent commit 3 months agopypi runjob} Downloads
Pysradb ⭐ 269
Package for fetching metadata and downloading data from SRA/ENA/GEO
dependent packages 7total releases 38latest release September 17, 2023most recent commit 7 months agopypi pysradb} Downloads
Nphase ⭐ 39
Ploidy agnostic phasing pipeline and algorithm
total releases 27latest release April 21, 2022most recent commit 4 months ago
Oliver ⭐ 36
An opinionated Cromwell orchestration manager.
total releases 27latest release November 20, 2021most recent commit a year ago
Pyrpipe ⭐ 25
Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
total releases 6latest release January 18, 2021most recent commit 3 years ago
R2g ⭐ 49
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
dependent packages 1total releases 6latest release November 23, 2020most recent commit 3 years agopypi r2g} Downloads
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