Alternatives and similar repositories for Pipeline-Standardization:

Users that are interested in Pipeline-Standardization are comparing it to the libraries listed below

• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 3 months ago
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆96Updated 2 years ago
• mozack / abra2
  ABRA2
  ☆92Updated 2 years ago
• gatk-workflows / gatk4-germline-snps-indels
  Workflows for germline short variant discovery with GATK4
  ☆134Updated 3 years ago
• Griffan / VerifyBamID
  VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
  ☆96Updated 8 months ago
• zstephens / neat-genreads
  NEAT read simulation tools
  ☆97Updated 2 years ago
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆150Updated 2 years ago
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆117Updated 5 years ago
• gatk-workflows / seq-format-conversion
  Workflows for converting between sequence data formats
  ☆38Updated 3 years ago
• KCCG / ClinSV
  Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
  ☆67Updated 5 months ago
• CRG-CNAG / CalliNGS-NF
  GATK RNA-Seq Variant Calling in Nextflow
  ☆132Updated 2 years ago
• stevekm / IGV-snapshot-automator
  Script to automatically create and run IGV snapshot batchscripts
  ☆140Updated 2 years ago
• RCollins13 / CNView
  Visualization and annotation of CNVs from population-scale whole-genome sequencing data
  ☆70Updated 7 years ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆157Updated 5 months ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆111Updated 7 months ago
• hall-lab / svtyper
  Bayesian genotyper for structural variants
  ☆127Updated 3 years ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆178Updated this week
• broadinstitute / gatk-docs
  Documentation archive for GATK tools and workflows
  ☆84Updated 5 years ago
• parklab / NGSCheckMate
  Software program for checking sample matching for NGS data
  ☆128Updated 7 months ago
• genome-in-a-bottle / giab_latest_release
  This repository contains information about latest release from Genome in a Bottle project
  ☆73Updated 5 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆156Updated last year
• 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…
  ☆52Updated 4 years ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆194Updated 3 years ago
• gymreklab / GangSTR
  A tool for profiling long STRs from short reads
  ☆94Updated 3 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆192Updated last year
• Illumina / ExpansionHunterDenovo
  A suite of tools for detecting expansions of short tandem repeats
  ☆80Updated last year
• nh13 / DWGSIM
  Whole Genome Simulator for Next-Generation Sequencing
  ☆96Updated 2 months ago
• imgag / ClinCNV
  Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
  ☆82Updated last week
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆240Updated 2 months ago
• compbiocore / VariantVisualization.jl
  Julia package powering VIVA, our tool for visualization of genomic variation data. Manual:
  ☆85Updated last year