Alternatives and similar repositories for TRexs

Users that are interested in TRexs are comparing it to the libraries listed below

• PacificBiosciences / sawfish
  Joint structural variant and copy number variant caller for HiFi sequencing data
  ☆64Updated 2 weeks ago
• schatzlab / crossstitch
  Code for phasing SVs with SNPs
  ☆52Updated 5 years ago
• ACEnglish / adotto
  Working space for the GIAB TR benchmarking project
  ☆23Updated last year
• EichlerLab / svpop
  Variant annotation and merging pipeline
  ☆39Updated 3 months ago
• PacificBiosciences / MethBat
  A battery of methylation tools for PacBio HiFi reads
  ☆43Updated last week
• 1kg-ont-vienna / sv-analysis
  SV analysis of the long-read sequencing data of the 1019 samples of the 1KG-ONT panel
  ☆37Updated 6 months ago
• PacificBiosciences / pbfusion
  ☆23Updated 5 months ago
• mcfrith / tandem-genotypes
  ☆49Updated last year
• MeHelmy / princess
  ☆83Updated 8 months ago
• ACEnglish / kanpig
  Kmer Analysis of Pileups for Genotyping
  ☆33Updated this week
• ChaissonLab / vamos
  VNTR annotation using motif selection
  ☆39Updated 2 months ago
• rrazaghi / modbamtools
  Set of tools to manipulate and visualize modified base bam files
  ☆57Updated 3 years ago
• Parsoa / SVDSS
  Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)
  ☆46Updated 2 months ago
• Illumina / witty.er
  What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
  ☆34Updated 2 years ago
• mrvollger / SDA
  Segmental Duplication Assembler (SDA).
  ☆44Updated 2 years ago
• jfarek / xatlas
  ☆31Updated 3 years ago
• fritzsedlazeck / Spectre
  Copy number caller for long read data including SNV utilization
  ☆68Updated 7 months ago
• KolmogorovLab / hapdiff
  SV calling for diploid assemblies
  ☆29Updated last year
• lh3 / panmask
  Easy genomic regions for short-read variant calling
  ☆45Updated 2 months ago
• mktle / colorSV
  somatic SV calling on matched tumor-normal co-assembly graphs
  ☆22Updated last year
• llecompte / SVJedi
  SV genotyping with long reads
  ☆40Updated 2 years ago
• smehringer / SViper
  Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.
  ☆32Updated 3 years ago
• Platinum-Pedigree-Consortium / Platinum-Pedigree-Datasets
  ☆35Updated 9 months ago
• alshai / levioSAM
  Lift-over alignments from variant-aware references
  ☆34Updated 2 years ago
• mkirsche / Iris
  A module for improving the insertion sequences of structural variant calls
  ☆32Updated 4 years ago
• kage-genotyper / kage
  Alignment-free genotyper for SNPs and short indels, implemented in Python.
  ☆52Updated 8 months ago
• UCSC-nanopore-cgl / MarginPolish
  MarginPolish: Graph based assembly polishing
  ☆47Updated 4 years ago
• andrewSharo / StrVCTVRE
  StrVCTVRE, a structural variant classifier for exonic deletions and duplications
  ☆19Updated last year
• treangenlab / methphaser
  MethPhaser: methylation-based haplotype phasing of human genomes
  ☆50Updated 8 months ago
• PacificBiosciences / svpack
  Structural variant (SV) analysis tools
  ☆39Updated last year