bioinformatics-pipeline
There are 634 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
Compute over Data framework for public, transparent, and optionally verifiable computation
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
flowhub-team/WholeGenomeSequencing-WGS
Whole Genome Sequencing analysis, WGS analysis
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/snp-sites
Finds SNP sites from a multi-FASTA alignment file
lynnlangit/gcp-for-bioinformatics
GCP for Bioinformatics Researchers
sanger-pathogens/circlator
A tool to circularize genome assemblies
kundajelab/atac_dnase_pipelines
ATAC-seq and DNase-seq processing pipeline
nickjcroucher/gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
sanger-pathogens/ariba
Antimicrobial Resistance Identification By Assembly
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
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.
yupenghe/methylpy
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
cbg-ethz/V-pipe
V-pipe is a pipeline designed for analysing NGS data of short viral genomes
GuyTeichman/RNAlysis
RNA sequencing analysis software
ShujiaHuang/ilus
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.
KarchinLab/open-cravat
A modular annotation tool for genomic variants
MaayanLab/Zika-RNAseq-Pipeline
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study
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.
mitoNGS/MToolBox
A bioinformatics pipeline to analyze mtDNA from NGS data
biowdl/tasks
A collection of reusable WDL tasks. Category:Other
urmi-21/pyrpipe
Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.
chanzuckerberg/czid-web
Infectious Disease Sequencing Platform
algbio/ggcat
Compacted and colored de Bruijn graph construction and querying
JetBrains-Research/snakecharm
Plugin for PyCharm / IntelliJ IDEA Platform IDEs which adds support for Snakemake language.
YichaoOU/HemTools
HemTools: a collection of NGS pipelines and bioinformatic analyses
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.
sanger-pathogens/assembly_improvement
Improve the quality of a denovo assembly by scaffolding and gap filling
sanger-pathogens/iva
de novo virus assembler of Illumina paired reads
sagnikbanerjee15/Finder
A fully automated gene annotator from RNA-Seq expression data