bioinformatics-pipeline
There are 704 repositories under bioinformatics-pipeline topic.
scipipe/scipipe
Robust, flexible and resource-efficient pipelines using Go and the commandline
grailbio/reflow
A language and runtime for distributed, incremental data processing in the cloud
bacalhau-project/bacalhau
Community-driven, simple, yet powerful framework for fast, cost-effective distributed Compute over Data.
sanger-pathogens/Roary
Rapid large-scale prokaryote pan genome analysis
saketkc/pysradb
Package for fetching metadata and downloading data from SRA/ENA/GEO
r3fang/SnapATAC
Analysis Pipeline for Single Cell ATAC-seq
lynnlangit/gcp-for-bioinformatics
GCP for Bioinformatics Researchers
sanger-pathogens/snp-sites
Finds SNP sites from a multi-FASTA alignment file
sanger-pathogens/Artemis
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
sanger-pathogens/circlator
A tool to circularize genome assemblies
flowhub-team/WholeGenomeSequencing-WGS
Whole Genome Sequencing analysis, WGS analysis
nickjcroucher/gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
hillerlab/TOGA
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.
sanger-pathogens/ariba
Antimicrobial Resistance Identification By Assembly
kundajelab/atac_dnase_pipelines
ATAC-seq and DNase-seq processing pipeline
vanheeringen-lab/seq2science
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.
ngless-toolkit/ngless
NGLess: NGS with less work
yupenghe/methylpy
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
ShujiaHuang/ilus
A lightweight and handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis by using GATK and Sentieon. 一个基于 GATK 和 Sentieon 的简易且全面的 WGS/WES 分析流程生成器.
cbg-ethz/V-pipe
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
GuyTeichman/RNAlysis
Analyze your RNA sequencing data without writing a single line of code
KarchinLab/open-cravat
A modular annotation tool for genomic variants
GregorySchwartz/too-many-cells
Cluster single cells and analyze cell clade relationships with colorful visualizations.
nsalomonis/altanalyze
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.
MaayanLab/Zika-RNAseq-Pipeline
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study
mitoNGS/MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS data
biowdl/tasks
A collection of reusable WDL tasks. Category:Other
algbio/ggcat
Compacted and colored de Bruijn graph construction and querying
chanzuckerberg/czid-web
Infectious Disease Sequencing Platform
urmi-21/pyrpipe
Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
twoXes/awesome-structural-bioinformatics
Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.
YichaoOU/HemTools
HemTools: a collection of NGS pipelines and bioinformatic analyses
stjude-rust-labs/sprocket
A bioinformatics workflow engine built on top of the Workflow Description Language (WDL).
JetBrains-Research/snakecharm
Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.
sagnikbanerjee15/Finder
A fully automated gene annotator from RNA-Seq expression data
sanger-pathogens/assembly_improvement
Improve the quality of a denovo assembly by scaffolding and gap filling