Alternatives and similar repositories for rtg-tools

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

• dkoboldt / varscan
  Variant calling and somatic mutation/CNV detection for next-generation sequencing data
  ☆159Updated 2 years ago
• ga4gh / benchmarking-tools
  Repository for the GA4GH Benchmarking Team work developing standardized benchmarking methods for germline small variant calls
  ☆201Updated 4 years ago
• snakemake-workflows / dna-seq-gatk-variant-calling
  This Snakemake pipeline implements the GATK best-practices workflow
  ☆253Updated last year
• ACEnglish / truvari
  Structural variant toolkit for VCFs
  ☆357Updated 3 weeks ago
• igvteam / igv-reports
  Python application to generate self-contained pages embedding IGV visualizations, with no dependency on original input files.
  ☆366Updated this week
• pcingola / SnpEff
  ☆277Updated 3 months ago
• PapenfussLab / gridss
  GRIDSS: the Genomic Rearrangement IDentification Software Suite
  ☆268Updated 2 weeks ago
• genome / bam-readcount
  Count bases in BAM/CRAM files
  ☆317Updated 3 years ago
• AstraZeneca-NGS / VarDict
  VarDict
  ☆200Updated last year
• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆379Updated last year
• luntergroup / octopus
  Bayesian haplotype-based mutation calling
  ☆311Updated 2 months ago
• abyzovlab / CNVnator
  a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
  ☆222Updated 3 years ago
• lgmgeo / AnnotSV
  Annotation and Ranking of Structural Variation
  ☆258Updated 2 months ago
• genome-in-a-bottle / giab_data_indexes
  This repository contains data indexes from NIST's Genome in a Bottle project.
  ☆248Updated last year
• Magdoll / cDNA_Cupcake
  Miscellaneous collection of Python and R scripts for processing Iso-Seq data
  ☆268Updated last year
• adamewing / bamsurgeon
  tools for adding mutations to existing .bam files, used for testing mutation callers
  ☆241Updated 7 months ago
• broadinstitute / gatk-sv
  A structural variation pipeline for short-read sequencing
  ☆188Updated this week
• ryanlayer / samplot
  Plot structural variant signals from many BAMs and CRAMs
  ☆543Updated 10 months ago
• brentp / vcfanno
  annotate a VCF with other VCFs/BEDs/tabixed files
  ☆377Updated last year
• suhrig / arriba
  Fast and accurate gene fusion detection from RNA-Seq data
  ☆241Updated 2 months ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆214Updated last month
• gatk-workflows / gatk4-germline-snps-indels
  Workflows for germline short variant discovery with GATK4
  ☆137Updated 4 years ago
• OpenGene / AfterQC
  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data
  ☆210Updated 5 years ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆270Updated 4 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆232Updated 4 years ago
• timflutre / trimmomatic
  Read trimming tool for Illumina NGS data.
  ☆136Updated 10 years ago
• gatk-workflows / gatk4-data-processing
  Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
  ☆151Updated 2 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆224Updated 3 weeks ago
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆252Updated 11 months ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆246Updated last week