Alternatives and similar repositories for rtg-tools

Users that are interested in rtg-tools are comparing it to the libraries listed below

• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆391Updated 3 months ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆271Updated 2 months ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆320Updated 3 years ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆556Updated last year
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆208Updated 4 years ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆280Updated 6 months ago
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆495Updated last month
• AstraZeneca-NGS / VarDict
  VarDict
  ☆201Updated last year
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆390Updated 3 years ago
• ACEnglish / truvari
  Structural variant toolkit for VCFs
  ☆391Updated this week
• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆403Updated 2 years ago
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆230Updated 3 years ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆284Updated 10 months ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆261Updated 2 years ago
• pcingola / SnpEff
  ☆295Updated last week
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆316Updated 3 years ago
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆321Updated last week
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆428Updated 6 months ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆165Updated 2 years ago
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆334Updated 3 years ago
• lh3 / wgsim
  Reads simulator
  ☆282Updated 4 years ago
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆247Updated last year
• philres / ngmlr
  NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on r…
  ☆305Updated last year
• Illumina / manta
  Structural variant and indel caller for mapped sequencing data
  ☆454Updated last month
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆201Updated 4 months ago
• gatk-workflows / gatk4-data-processing
  Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
  ☆159Updated 3 years ago
• genome-in-a-bottle / giab_data_indexes
  This repository contains data indexes from NIST's Genome in a Bottle project.
  ☆257Updated 2 years ago
• bedops / bedops
  BEDOPS: high-performance genomic feature operations
  ☆354Updated 7 months ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆249Updated 2 months ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆196Updated this week