Alternatives and similar repositories for rtg-tools

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

• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆317Updated 3 years ago
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆204Updated 4 years ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆272Updated 3 months ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆383Updated 2 weeks ago
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆318Updated this week
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• lh3 / wgsim
  Reads simulator
  ☆281Updated 4 years ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆262Updated this week
• ACEnglish / truvari
  Structural variant toolkit for VCFs
  ☆375Updated last week
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆227Updated 3 years ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆193Updated this week
• Illumina / strelka
  Strelka2 germline and somatic small variant caller
  ☆381Updated 3 years ago
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆545Updated last year
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆258Updated 2 years ago
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆244Updated 10 months ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆275Updated 7 months ago
• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆396Updated 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…
  ☆306Updated last year
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆377Updated 3 months ago
• genome-in-a-bottle / giab_data_indexes
  This repository contains data indexes from NIST's Genome in a Bottle project.
  ☆256Updated last year
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆485Updated last month
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆317Updated 2 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆246Updated this week
• pcingola / SnpEff
  ☆290Updated last week
• Illumina / ExpansionHunter
  A tool for estimating repeat sizes
  ☆197Updated last year
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆333Updated 3 years ago
• pezmaster31 / bamtools
  C++ API & command-line toolkit for working with BAM data
  ☆429Updated 3 months ago
• gatk-workflows / gatk4-data-processing
  Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
  ☆156Updated 3 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆163Updated 2 years ago
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆199Updated last month