Alternatives and similar repositories for rtg-tools:

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

• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆268Updated last year
• ACEnglish / truvari
  Structural variant toolkit for VCFs
  ☆355Updated last week
• AstraZeneca-NGS / VarDict
  VarDict
  ☆198Updated last year
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆203Updated 4 years ago
• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆157Updated 2 years ago
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆221Updated 3 years ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆187Updated this week
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆253Updated last year
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆312Updated last month
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆541Updated 9 months ago
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆240Updated 6 months ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆268Updated 3 months ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆375Updated last year
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆315Updated 3 years ago
• pcingola / SnpEff
  ☆272Updated 2 months ago
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆362Updated 4 months ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆246Updated last month
• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆378Updated last year
• hall-lab / speedseq
  A flexible framework for rapid genome analysis and interpretation
  ☆316Updated 2 years ago
• gatk-workflows / gatk4-data-processing
  Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
  ☆150Updated 2 years ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆252Updated last month
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆201Updated this week
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆265Updated last year
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆227Updated 4 years ago
• lh3 / wgsim
  Reads simulator
  ☆274Updated 3 years ago
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆238Updated last month
• arq5x / lumpy-sv
  lumpy: a general probabilistic framework for structural variant discovery
  ☆325Updated 2 years ago
• hartwigmedical / hmftools
  Various algorithms for analysing genomics data
  ☆222Updated this week
• bioinform / somaticseq
  An ensemble approach to accurately detect somatic mutations using SomaticSeq
  ☆196Updated 2 weeks ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆196Updated 4 years ago