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
  ☆69Updated 2 months ago
• 1kg-ont-vienna / sv-analysis
  SV analysis of the long-read sequencing data of the 1019 samples of the 1KG-ONT panel
  ☆38Updated 9 months ago
• EichlerLab / svpop
  Variant annotation and merging pipeline
  ☆41Updated 6 months ago
• smehringer / SViper
  Swipe your Structural Variants called on long (ONT/PacBio) reads with short exact (Illumina) reads.
  ☆32Updated 3 years ago
• rrazaghi / modbamtools
  Set of tools to manipulate and visualize modified base bam files
  ☆58Updated 3 years ago
• mcfrith / tandem-genotypes
  ☆51Updated last year
• 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
• PacificBiosciences / MethBat
  A battery of methylation tools for PacBio HiFi reads
  ☆47Updated last month
• MeHelmy / princess
  ☆84Updated 10 months ago
• Platinum-Pedigree-Consortium / Platinum-Pedigree-Datasets
  ☆38Updated 2 weeks ago
• Sentieon / hap-eval
  A VCF comparison engine for structual variant benchmarking
  ☆23Updated 4 months ago
• ACEnglish / kanpig
  Kmer Analysis of Pileups for Genotyping
  ☆35Updated last week
• treangenlab / methphaser
  MethPhaser: methylation-based haplotype phasing of human genomes
  ☆52Updated 10 months ago
• EichlerLab / smrtsv2
  Structural variant caller
  ☆55Updated 4 years ago
• monarch-initiative / SvAnna
  Efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing
  ☆39Updated 2 months ago
• fritzsedlazeck / Spectre
  Copy number caller for long read data including SNV utilization
  ☆68Updated 10 months ago
• andrewSharo / StrVCTVRE
  StrVCTVRE, a structural variant classifier for exonic deletions and duplications
  ☆19Updated 2 years ago
• KolmogorovLab / hapdiff
  SV calling for diploid assemblies
  ☆30Updated last year
• ChaissonLab / vamos
  VNTR annotation using motif selection
  ☆39Updated last week
• Parsoa / SVDSS
  Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)
  ☆47Updated 4 months ago
• mrvollger / SDA
  Segmental Duplication Assembler (SDA).
  ☆44Updated 2 years ago
• PacificBiosciences / pbfusion
  ☆23Updated 8 months ago
• jts / smrest
  Tumour-only somatic mutation calling using long reads
  ☆28Updated last year
• ryanlayer / stix
  Structural Variant Index
  ☆75Updated last year
• lh3 / htsbox
  My experimental tools on top of htslib. NOT OFFICIAL!!!
  ☆59Updated 4 months ago
• lh3 / dipcall
  Reference-based variant calling pipeline for a pair of phased haplotype assemblies
  ☆105Updated 4 years ago
• shilpagarg / DipAsm
  ☆78Updated 5 years ago
• hitbc / gcSV
  ☆21Updated 2 weeks ago
• Illumina / witty.er
  What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
  ☆36Updated 2 years ago