Alternatives and similar repositories for SVE

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

• hall-lab / sv-pipeline
  Pipeline for structural variation detection in cohorts
  ☆49Updated 3 years ago
• EichlerLab / smrtsv2
  Structural variant caller
  ☆55Updated 3 years ago
• zeeev / mergeSVcallers
  heuristics to merge structural variant calls in VCF format.
  ☆36Updated 8 years ago
• talkowski-lab / svtk
  ☆35Updated 4 years ago
• DecodeGenetics / svimmer
  Structural variant merging tool
  ☆53Updated last year
• adamewing / tldr
  Identify and annotate TE-mediated insertions in long-read sequence data
  ☆42Updated last month
• scottgigante / haplotyped-methylome
  Reproducibility workflow for Gigante et al., 2018: Using long-read sequencing to detect imprinted DNA methylation
  ☆23Updated 6 years ago
• ksahlin / ultra
  Long-read splice alignment with high accuracy
  ☆64Updated 11 months ago
• jbelyeu / SV-plaudit
  Pipeline for structural variant image curation and analysis.
  ☆48Updated 3 years ago
• brwnj / covviz
  Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata
  ☆58Updated 3 years ago
• schatzlab / crossstitch
  Code for phasing SVs with SNPs
  ☆52Updated 5 years ago
• mskilab-org / gGnome
  R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
  ☆41Updated 3 weeks ago
• lh3 / etrf
  Exact Tandem Repeat Finder (not a TRF replacement)
  ☆49Updated 5 years ago
• HipSTR-Tool / HipSTR
  Genotype and phase short tandem repeats using Illumina whole-genome sequencing data
  ☆32Updated 4 years ago
• LeanQ / SPLITREADER
  Split-read pipeline for the identification of non-reference TE insertions with TSDs
  ☆25Updated 4 years ago
• timplab / nanopore-methylation-utilities
  ☆29Updated 4 years ago
• cortes-ciriano-lab / ReConPlot
  ☆23Updated 8 months ago
• czc / nb_distribution
  novoBreak: local assembly for breakpoint detection in cancer genomes
  ☆26Updated 7 years ago
• bioinform / metasv
  MetaSV: An accurate and integrative structural-variant caller for next generation sequencing
  ☆57Updated 8 years ago
• jts / methylation-analysis
  ☆45Updated 8 years ago
• liusihan / seGMM
  A new tool to infer sex from massively parallel sequencing data.
  ☆17Updated 3 months ago
• ljdursi / mergevcf
  Python package and routines for merging VCF files
  ☆29Updated 4 years ago
• JialiUMassWengLab / TEMP
  TEMP is a software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing dat…
  ☆22Updated 8 years ago
• rdemolgen / SavvySuite
  Suite of tools for analysing off-target reads to find CNVs, homozygous regions, and shared haplotypes
  ☆30Updated 2 weeks ago
• EichlerLab / svpop
  Variant annotation and merging pipeline
  ☆39Updated last month
• LappalainenLab / lorals
  ☆36Updated 2 years ago
• TomSkelly / MatchAnnot
  Python scripts for matching output of Pacific Biosciences IsoSeq RNA-seq pipeline to an annotation file.
  ☆23Updated 9 years ago
• talkowski-lab / gnomad-sv-pipeline
  Code and custom scripts relevant to gnomAD-SV (Collins*, Brand*, et al., 2020)
  ☆36Updated 5 years ago
• tk2 / RetroSeq
  RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference…
  ☆67Updated 2 years ago
• fritzsedlazeck / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆48Updated 5 years ago