Alternatives and similar repositories for rare-disease-wf:

Users that are interested in rare-disease-wf are comparing it to the libraries listed below

• fakedrtom / SVAFotate
  ☆39Updated 4 months ago
• HudsonAlpha / CSL_public_benchmark
  Location of public benchmarking; primarily final results
  ☆18Updated 2 years ago
• Illumina / witty.er
  What is true, thank you, ernestly. A large variant benchmarking tool analogous to hap.py for small variants.
  ☆30Updated last year
• Clinical-Genomics / BALSAMIC
  Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer
  ☆45Updated this week
• ChristopherWilks / megadepth
  BigWig and BAM utilities
  ☆92Updated 10 months ago
• bioinform / metasv
  MetaSV: An accurate and integrative structural-variant caller for next generation sequencing
  ☆55Updated 7 years ago
• cancerit / alleleCount
  Support code for NGS copy number algorithms. Takes a file of locations and a [cr|b]am file and generates a count of coverage of each alle…
  ☆43Updated 2 years ago
• fritzsedlazeck / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆46Updated 4 years ago
• genepi / haplocheck
  Phylogeny-based Contamination Detection in Mitochondrial and Whole-Genome Sequencing Studies
  ☆18Updated last year
• talkowski-lab / gnomad-sv-pipeline
  Code and custom scripts relevant to gnomAD-SV (Collins*, Brand*, et al., 2020)
  ☆36Updated 4 years ago
• hall-lab / sv-pipeline
  Pipeline for structural variation detection in cohorts
  ☆49Updated 3 years ago
• TheJacksonLaboratory / SVE
  ☆51Updated 5 years ago
• kcleal / dysgu
  Toolkit for calling structural variants using short or long reads
  ☆100Updated 2 weeks ago
• SciLifeLab / TIDDIT
  TIDDIT - structural variant calling
  ☆73Updated last week
• wdecoster / nano-snakemake
  A snakemake pipeline for SV analysis from nanopore genome sequencing
  ☆51Updated 4 years ago
• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆42Updated 2 years ago
• monarch-initiative / SvAnna
  Efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing
  ☆35Updated 7 months ago
• mskilab-org / JaBbA
  MIP based joint inference of copy number and rearrangement state in cancer whole genome sequence data.
  ☆56Updated 7 months ago
• zeeev / mergeSVcallers
  heuristics to merge structural variant calls in VCF format.
  ☆35Updated 8 years ago
• PacificBiosciences / svpack
  Structural variant (SV) analysis tools
  ☆35Updated 6 months ago
• rrazaghi / modbamtools
  Set of tools to manipulate and visualize modified base bam files
  ☆49Updated 2 years ago
• DecodeGenetics / svimmer
  Structural variant merging tool
  ☆49Updated 5 months ago
• GooglingTheCancerGenome / sv-callers
  Snakemake-based workflow for detecting structural variants in genomic data
  ☆79Updated 11 months ago
• nspies / svviz2
  for visual evaluation of read support for structural variation
  ☆51Updated 7 months ago
• rdemolgen / SavvySuite
  Suite of tools for analysing off-target reads to find CNVs, homozygous regions, and shared haplotypes
  ☆27Updated 6 months ago
• ljdursi / mergevcf
  Python package and routines for merging VCF files
  ☆29Updated 3 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…
  ☆65Updated 2 years ago
• nygenome / Conpair
  Concordance and contamination estimator for tumor–normal pairs
  ☆56Updated 3 months ago
• ctsa / svtools
  Tools for processing and analyzing structural variants.
  ☆32Updated 9 years ago
• LosicLab / starchip
  Detection of Circular RNA and Fusions from RNA-Seq
  ☆32Updated 6 years ago