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Bioinformatics Pipeline
65 Open Source Bioinformatics Pipeline Software Projects
Free and open source bioinformatics pipeline code projects including engines, APIs, generators, and tools.
Scipipe
780 ⭐
Robust, flexible and resource-efficient pipelines using Go and the commandline
Reflow
673 ⭐
A language and runtime for distributed, incremental data processing in the cloud
Snapatac
164 ⭐
Analysis Pipeline for Single Cell ATAC-seq
Roary
161 ⭐
Rapid large-scale prokaryote pan genome analysis
Atac_dnase_pipelines
141 ⭐
ATAC-seq and DNase-seq processing pipeline
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
Snp Sites
112 ⭐
Finds SNP sites from a multi-FASTA alignment file
Circlator
111 ⭐
A tool to circularize genome assemblies
Ngless
110 ⭐
NGLess: NGS with less work
Pysradb
113 ⭐
Package for fetching metadata and downloading data from SRA/ENA
Ariba
90 ⭐
Antimicrobial Resistance Identification By Assembly
Gcp For Bioinformatics
84 ⭐
GCP Essentials for Bioinformatics Researchers
Zika Rnaseq Pipeline
81 ⭐
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study
Methylpy
67 ⭐
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
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.
Open Cravat
54 ⭐
A modular annotation tool for genomic variants
Idseq Web
50 ⭐
Infectious Disease Sequencing Platform
Too Many Cells
49 ⭐
Cluster single cells and analyze cell clade relationships with colorful visualizations.
Mtoolbox
44 ⭐
A bioinformatics pipeline to analyze mtDNA from NGS data
Eoulsan
40 ⭐
A pipeline and a framework for NGS analysis (RNA-Seq and soon Chip-Seq)
Assembly_improvement
39 ⭐
Improve the quality of a denovo assembly by scaffolding and gap filling
Sanger Pathogens Iva
36 ⭐
de novo virus assembler of Illumina paired reads
Snakecharm
36 ⭐
Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.
Biowdl Tasks
35 ⭐
A collection of reusable WDL tasks. Category:Other
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.
Lixiangchun Mynotebook
31 ⭐
My daily notebook on bioinformatic data analysis and machine learning
Bystro
29 ⭐
Bystro genetic analysis (annotation, filtering, statistics)
Skymap
29 ⭐
High-throughput gene to knowledge mapping through massive integration of public sequencing data.
Databio Pypiper
27 ⭐
Python toolkit for building restartable pipelines
Biokepi
26 ⭐
Bioinformatics Ketrew Pipelines
Gff3toembl
23 ⭐
Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
Tiptoft
23 ⭐
Predict plasmids from uncorrected long read data
Bioqueue
22 ⭐
A novel pipeline framework to accelerate bioinformatics analysis
Snatac
21 ⭐
<<------ Use SnapATAC!!
Plasmidtron
21 ⭐
Assembling the cause of phenotypes and genotypes from NGS data
Phigaro
24 ⭐
Phigaro is a scalable command-line tool for predicting phages and prophages
Nb_distribution
21 ⭐
novoBreak: local assembly for breakpoint detection in cancer genomes
Genomedisco
19 ⭐
Software for comparing contact maps from HiC, CaptureC and other 3D genome data.
Fyrd
18 ⭐
Submit functions and shell scripts to torque and slurm clusters or local machines using python.
Grein
20 ⭐
GREIN : GEO RNA-seq Experiments Interactive Navigator
Nf Core Cookiecutter
18 ⭐
DEPRECIATED! Please use nf-core/tools instead
Workflows
18 ⭐
Bioinformatics curated workflows that use Biocontainers tools
Metasub_cap
17 ⭐
A comprehensive pipeline for short read metagenomic data
Deplanckelab Asap
16 ⭐
ASAP : Automated Single-cell Analysis Pipeline
Oliver
16 ⭐
An opinionated Cromwell orchestration manager.
Saffrontree
16 ⭐
SaffronTree: Reference free rapid phylogenetic tree construction from raw read data
Cd4 Csaw
16 ⭐
Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set
Consensustme
16 ⭐
ConsensusTME Gene Sets and R Script
Meta Proteome Analyzer
16 ⭐
MetaProteomeAnalyzer (MPA) software for analyzing and visualizing MS-based metaproteomics data.
Sentieon Dnaseq
14 ⭐
Sentieon DNAseq
Mlst_check
13 ⭐
Multilocus sequence typing by blast using the schemes from PubMLST
Streamformatics
13 ⭐
Real-time species-typing visualisation for nanopore data.
Socru
12 ⭐
Order and orientation of complete bacterial genomes
Circompara
12 ⭐
:microscope: A multi-method comparative bioinformatics pipeline to detect and study circRNAs from RNA-seq data
Looper
11 ⭐
A job submitter for Portable Encapsulated Projects
Klugem Watchdog
11 ⭐
Workflow management system for the automated and distributed analysis of large-scale experimental data.
Guidock
11 ⭐
Graphical GUI for Docker (Bioconductor, R, Cytoscape, NetworkBMA)
Lsf
11 ⭐
Snakemake profile for running jobs on an LSF cluster
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.
Blss
11 ⭐
A suite of unique bioinformatics tools for the brave explorer.
Chipimputation
10 ⭐
Genotype Imputation Pipeline for H3Africa
Bio Tradis
10 ⭐
A set of tools to analyse the output from TraDIS analyses
Scanpav
10 ⭐
Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
Ilus
17 ⭐
A handy pipeline generator for whole genome re-sequencing (WGS) and whole exom sequencing data (WES) analysis.