Alternatives and similar repositories for genipe

Users that are interested in genipe are comparing it to the libraries listed below

• broadinstitute / oncotator
  ☆69Updated 3 years ago
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 10 years ago
• gatk-workflows / gatk4-somatic-snvs-indels
  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory. The workflows are al…
  ☆78Updated 5 years ago
• gatk-workflows / five-dollar-genome-analysis-pipeline
  Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline
  ☆57Updated 6 years ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆74Updated 4 years ago
• SciLifeLab / NGI-RNAseq
  Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.
  ☆51Updated 7 years ago
• Clinical-Genomics / genmod
  Annotate models of genetic inheritance patterns in variant files (vcf files)
  ☆85Updated 3 weeks ago
• broadinstitute / mutect
  MuTect -- Accurate and sensitive cancer mutation detection
  ☆102Updated 2 years ago
• cancerit / cgpBattenberg
  Battenberg algorithm and associated implementation script
  ☆53Updated 5 years ago
• jdidion / atropos
  An NGS read trimming tool that is specific, sensitive, and speedy. (production)
  ☆126Updated 9 months ago
• imgag / ClinCNV
  Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
  ☆91Updated 4 months ago
• gatk-workflows / broad-prod-wgs-germline-snps-indels
  Workflows for germline short variant discovery in WGS data. PairedEndSingleSampleWf has been superseded in Broad production by https://gi…
  ☆57Updated 5 years ago
• cbg-ethz / NGS-pipe
  NGS-pipe: next-generation sequencing pipelines for precision oncology
  ☆114Updated 6 years ago
• rhshah / IMPACT-Pipeline
  Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
  ☆57Updated 4 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• gavinha / TitanCNA
  Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
  ☆100Updated 4 years ago
• macarthur-lab / igv_utils
  utilities for working with IGV: opening files remotely in either desktop IGV or a web viewer (igv.js), creating screenshots, etc.
  ☆49Updated 6 years ago
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated last year
• zhanxw / checkVCF
  Sanity check Variant Call Format (VCF) files.
  ☆37Updated 9 years ago
• mhguo1 / TRAPD
  Burden testing against public controls
  ☆50Updated last year
• deaconjs / ThousandVariantCallersRepo
  Thousand Variant Callers Project Repository
  ☆74Updated 6 years ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆99Updated 3 years ago
• hartleys / QoRTs
  Quality of RNA-Seq Toolset
  ☆53Updated 6 years ago
• CGATOxford / cgat
  Do not use - please refer to our newest code: https://github.com/cgat-developers/cgat-apps
  ☆124Updated 7 years ago
• WGLab / Phen2Gene
  Phenotype driven gene prioritization for HPO
  ☆51Updated 4 years ago
• statgen / gotcloud
  Genomes on the Cloud, Mapping & Variant Calling Pipelines
  ☆33Updated 8 years ago
• ratschlab / spladder
  Tool for the detection and quantification of alternative splicing events from RNA-Seq data.
  ☆111Updated 6 months ago
• ChristofferFlensburg / superFreq
  Analysis pipeline for cancer sequencing data
  ☆112Updated 9 months ago
• sigven / gvanno
  Generic human DNA variant annotation pipeline
  ☆59Updated last year
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆117Updated last year