65 Open Source Bioinformatics Pipeline Software Projects
Free and open source bioinformatics pipeline code projects including engines, APIs, generators, and tools.
Sanger Pathogens Artemis 128 ⭐
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
Zika Rnaseq Pipeline 81 ⭐
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study
Gubbins 61 ⭐
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Altanalyze 56 ⭐
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.
Too Many Cells 49 ⭐
Cluster single cells and analyze cell clade relationships with colorful visualizations.
Snakecharm 36 ⭐
Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.
Seq2science 39 ⭐
Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and RNA-seq workflows. Works equally easy with public as local data.
Skymap 29 ⭐
High-throughput gene to knowledge mapping through massive integration of public sequencing data.
Fyrd 18 ⭐
Submit functions and shell scripts to torque and slurm clusters or local machines using python.
Saffrontree 16 ⭐
SaffronTree: Reference free rapid phylogenetic tree construction from raw read data
Meta Proteome Analyzer 16 ⭐
MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.
Circompara 12 ⭐
:microscope: A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data
Klugem Watchdog 11 ⭐
Workflow management system for the automated and distributed analysis of large-scale experimental data.
Speciesprimer 11 ⭐
The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.
Scanpav 10 ⭐
Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.