Alternatives and similar repositories for GATK-pipeline

Users that are interested in GATK-pipeline are comparing it to the libraries listed below

• jkbonfield / crumble

  View on GitHub
  Exploration of controlled loss of quality values for compressing CRAM files
  ☆36Feb 23, 2023Updated 2 years ago
• AllonKleinLab / LARRY

  View on GitHub
  ☆19Jun 16, 2023Updated 2 years ago
• lulab / lulab.github.io

  View on GitHub
  Lu Lab @ Tsinghua University
  ☆19Nov 11, 2025Updated 3 months ago
• joachimwolff / scHiCExplorer

  View on GitHub
  Single-cell Hi-C data analysis toolbox
  ☆27Aug 13, 2021Updated 4 years ago
• gkudla / hyb

  View on GitHub
  hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data
  ☆13Jul 12, 2024Updated last year
• evolgeniusteam / EvolviewDocumentation

  View on GitHub
  Documentation for Evolview
  ☆29Nov 27, 2021Updated 4 years ago
• griffithlab / rnaseq_tutorial_wiki

  View on GitHub
  The wiki repo, with pull request enabled, for the rnaseq_tutorial
  ☆26May 7, 2020Updated 5 years ago
• BackofenLab / CRISPRtracrRNA

  View on GitHub
  ☆10Mar 6, 2025Updated 11 months ago
• DRL / kinfin

  View on GitHub
  Taxon-aware analysis of clustered protein sequences
  ☆31Jul 1, 2024Updated last year
• melbournebioinformatics / variant_calling_pipeline

  View on GitHub
  A simple variant calling and annotation pipeline using BWA, GATK and ENSEMBL. This version of the pipeline uses the Rubra/Ruffus framewor…
  ☆34Mar 18, 2014Updated 11 years ago
• fhalab / LevSeq

  View on GitHub
  Pipeline for Nanopore sequencing: demultiplexing, variant calling, and quality visualization with error handling.
  ☆10Jan 25, 2026Updated 3 weeks ago
• caochch / RIC-seq

  View on GitHub
  Perl scripts for analysis RIC-seq data
  ☆11Feb 6, 2020Updated 6 years ago
• ZhuangLab / 3D-printing

  View on GitHub
  Designs for 3D printed parts that were developed in the Zhuang Lab.
  ☆11Dec 2, 2020Updated 5 years ago
• juansearch / callMom

  View on GitHub
  Python script for calling SNPs, MNPs, and indels in mitochondrial DNA.
  ☆10Apr 19, 2016Updated 9 years ago
• maximilianh / ucscBeacon

  View on GitHub
  A GA4GH Draft Beacon implementation
  ☆11Oct 23, 2015Updated 10 years ago
• malabz / HAlign-G

  View on GitHub
  A rapid and low-memory multiple-genome aligner for closely related genomes
  ☆24Sep 3, 2025Updated 5 months ago
• dwimperl / perl-5.14.2.1-32bit-windows

  View on GitHub
  ☆11Mar 13, 2012Updated 13 years ago
• goodarzilab / pyteiser

  View on GitHub
  Python implementation of TEISER also capable of using SHAPE structural probing data
  ☆12Jan 7, 2025Updated last year
• ISUgenomics / common_analyses

  View on GitHub
  Repository of common bioinformatics scripts
  ☆39Sep 21, 2021Updated 4 years ago
• AlphaGenes / AlphaImpute2

  View on GitHub
  AlphaImpute2: pedigree- and population-based genotype imputation
  ☆12Dec 19, 2025Updated last month
• huangwenze / PrismNet_analysis

  View on GitHub
  the analysis script for PrismNet
  ☆10May 17, 2020Updated 5 years ago
• morispi / HG-CoLoR

  View on GitHub
  Hybrid method based on a variable-order de bruijn Graph for the error Correction of Long Reads
  ☆11Jan 20, 2021Updated 5 years ago
• JaneliaSciComp / msg

  View on GitHub
  Multiplexed Shotgun Genotyping
  ☆11Feb 15, 2022Updated 4 years ago
• guyleonard / gene_prediction_pipeline

  View on GitHub
  Gene Prediction using MAKER, CEGMA, SNAP, GENEMARK & AUGUSTUS
  ☆10Jul 20, 2017Updated 8 years ago
• lh3 / bioseq-js

  View on GitHub
  For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml
  ☆39Aug 8, 2019Updated 6 years ago
• berkorbay / ibb

  View on GitHub
  R package wrapper for Istanbul Municipality Open Data Portal
  ☆10Apr 24, 2021Updated 4 years ago
• theislab / gastrulation_analysis

  View on GitHub
  ☆10Jun 25, 2021Updated 4 years ago
• HMPNK / CSA2.6

  View on GitHub
  Chromosome Scale Assembler: A high-throughput chromosome scale genome assembly pipeline for vertebrate genomes
  ☆10Oct 16, 2024Updated last year
• lvclark / polysat

  View on GitHub
  polysat 1.7: tools for polyploid microsatellite analysis
  ☆12Dec 20, 2024Updated last year
• Bioconductor / CSAMA2015

  View on GitHub
  Course material for CSAMA 2015: Statistics and Computing in Genome Data Science
  ☆11Mar 15, 2023Updated 2 years ago
• ajank / balancer-paper

  View on GitHub
  Computational analyses of WGS, mate-pair, RNA-seq, Hi-C and Capture-C data from highly rearranged balancer chromosomes in Drosophila mela…
  ☆10Sep 25, 2019Updated 6 years ago
• IARCbioinfo / mutspec

  View on GitHub
  Mutation Spectra Analysis
  ☆10Mar 15, 2018Updated 7 years ago
• veltenlab / PrimerDesign

  View on GitHub
  Package to design primers for MutaSeq and related methods
  ☆11Jan 15, 2021Updated 5 years ago
• dariober / ASCIIGenome

  View on GitHub
  Text Only Genome Viewer!
  ☆231Updated this week
• likelet / LncPipe

  View on GitHub
  A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq datasets
  ☆84Oct 22, 2022Updated 3 years ago
• guigolab / grape-nf

  View on GitHub
  An automated RNA-seq pipeline using Nextflow
  ☆37Dec 17, 2025Updated last month
• dekkerlab / matrix_paper

  View on GitHub
  Scripts and notebooks used in Akgol Oksuz et al. paper
  ☆11Jan 18, 2021Updated 5 years ago
• davidrequena / multifastats

  View on GitHub
  Multifastats: Multi-Fasta Sequence Stats. Free python-based program that, from a set of a set of 'fasta' sequences (as group or individua…
  ☆10Feb 21, 2018Updated 7 years ago
• MrDannyWu / PythonCrawler

  View on GitHub
  This repository is some small projects for DannyWu learning python crawlers.Welcome your visit and hope to learn together!
  ☆10Dec 12, 2021Updated 4 years ago