89 Open Source Bioinformatics Pipeline Software Projects
Free and open source bioinformatics pipeline code projects including engines, APIs, generators, and tools.
Sanger Pathogens Artemis 160 ⭐
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 87 ⭐
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study
Gubbins 83 ⭐
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
Altanalyze 69 ⭐
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 66 ⭐
Cluster single cells and analyze cell clade relationships with colorful visualizations.
Snakecharm 45 ⭐
Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.
Seq2science 81 ⭐
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.
Skymap 29 ⭐
High-throughput gene to knowledge mapping through massive integration of public sequencing data.
Fyrd 19 ⭐
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 18 ⭐
MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.
Circompara 13 ⭐
:microscope: A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data
Klugem Watchdog 12 ⭐
Workflow management system for the automated and distributed analysis of large-scale experimental data.
Speciesprimer 20 ⭐
The SpeciesPrimer pipeline is intended to help researchers finding specific primer pairs for the detection and quantification of bacterial species in complex ecosystems.
Scanpav 18 ⭐
Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
Ilus 54 ⭐
A handy variant calling pipeline generator for whole genome re-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.
Yangwu91 R2g 48 ⭐
A homology-based, computationally lightweight pipeline for discovering genes in the absence of an assembly
Pyrpipe 45 ⭐
Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
Grupo Estudo Bioinformatica 23 ⭐
Repositório do grupo de estudo de Bioinformática da rede de comunidades das PyLadies Brasil.
Novartis Pisces 18 ⭐
PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.
Toga 24 ⭐
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.
Positive Selection 13 ⭐
Scripts and procedures for detecting positively selected genes and codons in primates
Bgi Full Length Rna Analysis Pipeline 12 ⭐
Full-Length RNA Analysis pipeline developted by BGI RD group.
Tes_genes_relationship_pipeline 12 ⭐
Distribution of TEs and their relationship to genes in host genome
Riboraptor 12 ⭐
Tool for ribo-seq analysis. Most of the functionality moved to ribotricer (https://github.com/smithlabcode/ribotricer)
Igdiscover 10 ⭐
Analyze antibody repertoires and discover new V genes from high-throughput sequencing reads
Macse_v2_pipelines 11 ⭐
This repository provides source code for several pipelines dedicated to the alignment of nucleotide coding sequences that are based on MACSE. These pipelines are mostly bash scripts encapsulated within singularity containers and sometimes combined in nextflow workflows.
Rnaseq Pipeline 12 ⭐
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
Omicselector 10 ⭐
OmicSelector - Environment, docker-based application and R package for biomarker signiture selection (feature selection) & deep learning diagnostic tool development from high-throughput high-throughput omics experiments and other multidimensional datasets. Initially developed for miRNA-seq, RNA-seq and qPCR.