Alternatives and similar repositories for five-dollar-genome-analysis-pipeline

Users that are interested in five-dollar-genome-analysis-pipeline are comparing it to the libraries listed below

• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆98Updated 3 years 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 PairedEndSingleSampleWf has been superseded in Broad production by https://gi…
  ☆56Updated 5 years ago
• cc2qe / vawk
  An awk-like VCF parser
  ☆56Updated last year
• bahlolab / bioinfotools
  Documenting usage and experience with bioinformatic tools
  ☆40Updated 9 years ago
• relipmoc / skewer
  ☆95Updated 2 years ago
• PapenfussLab / StructuralVariantAnnotation
  R package designed to simplify structural variant analysis
  ☆73Updated 3 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
• gatk-workflows / gatk4-exome-analysis-pipeline
  This WDL pipeline implements data pre-processing and initial variant calling according to the GATK Best Practices for germline SNP and In…
  ☆55Updated 4 years ago
• ccagc / QDNAseq
  QDNAseq package for Bioconductor
  ☆50Updated last year
• svviz / svviz
  Read visualizer for structural variants
  ☆84Updated 7 years ago
• arq5x / bedtools-protocols
  ☆78Updated 11 years ago
• gt1 / biobambam2
  Tools for early stage alignment file processing
  ☆95Updated 6 years ago
• vplagnol / ExomeDepth
  ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.
  ☆73Updated last month
• jdidion / atropos
  An NGS read trimming tool that is specific, sensitive, and speedy. (production)
  ☆122Updated 4 months ago
• 10XGenomics / supernova
  10x Genomics Linked-Read Diploid De Novo Assembler
  ☆65Updated 6 years ago
• GenomiqueENS / dockerfiles
  ☆82Updated 3 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  This repo has been archived, these workflows are still available in the GATK repository under the scripts directory.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…
  ☆77Updated 5 years ago
• nygenome / Conpair
  Concordance and contamination estimator for tumor–normal pairs
  ☆58Updated 10 months ago
• RCollins13 / CNView
  Visualization and annotation of CNVs from population-scale whole-genome sequencing data
  ☆72Updated 7 years ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆71Updated 11 months ago
• CCDG / Pipeline-Standardization
  ☆82Updated 6 years ago
• IARCbioinfo / needlestack
  Multi-sample somatic variant caller
  ☆52Updated 3 years ago
• deaconjs / ThousandVariantCallersRepo
  Thousand Variant Callers Project Repository
  ☆73Updated 5 years ago
• dnanexus-archive / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆103Updated 4 years ago
• dantaki / SV2
  Support Vector Structural Variation Genotyper
  ☆58Updated 5 years ago
• PubuduSaneth / cnvScan
  CNV screening and annotation tool
  ☆25Updated 8 years ago
• gatk-workflows / seq-format-conversion
  Workflows for converting between sequence data formats
  ☆38Updated 3 years ago
• slzhao / QC3
  QC3, a quality control tool designed for DNA sequencing data for raw data, alignment, and variant calling.
  ☆32Updated 9 years ago
• mozack / abra
  Assembly Based ReAligner
  ☆74Updated 7 years ago
• genome-in-a-bottle / giab_latest_release
  This repository contains information about latest release from Genome in a Bottle project
  ☆74Updated 5 years ago