Alternatives and similar repositories for CaVEMaN

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

• gzhmat / ShinyCNV
  a Shiny/R application to view and annotate copy number variations
  ☆28Updated 2 years ago
• fritzsedlazeck / SURVIVOR_ant
  A framework to annotate SVs with previous known SVs (vcf file) and or with genomic features (gff and or bed files)
  ☆13Updated 7 years ago
• aquaskyline / 16GT
  Simultaneous detection of SNPs and Indels using a 16-genotype probabilistic model
  ☆27Updated last year
• Kingsford-Group / squid
  SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data
  ☆42Updated 3 years ago
• vsbuffalo / snakemake-tutorial
  Snakemake tutorial materials
  ☆19Updated 5 years ago
• griffithlab / VAtools
  A set of tools to annotate VCF files with expression and readcount data
  ☆29Updated 9 months ago
• ernfrid / diagnose_dups
  A tool to examine duplicate read characteristics in a BAM file
  ☆12Updated 8 years ago
• arq5x / grabix
  a wee tool for random access into BGZF files.
  ☆85Updated 7 years ago
• seandavi / GFFutils
  Convert, explore, and manipulate GFF and GTF files (used in bioinformatics) using a sqlite-based approach
  ☆36Updated 14 years ago
• Transipedia / dekupl
  Exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.
  ☆15Updated 7 years ago
• smshuai / DriverPower
  DriverPower
  ☆26Updated 10 months ago
• cdarby / samovar
  Somatic (mosaic) SNV caller for 10X Genomics data using random forest classification and feature-based filters
  ☆23Updated 6 years ago
• J35P312 / FindSV
  Structural variant pipeline
  ☆17Updated 5 years ago
• quinlan-lab / ccrhtml
  A small repo for storing the code for making the files and html for CCRs.
  ☆22Updated 6 years ago
• umccr / vcf_stuff
  📊Evaluating, filtering, comparing, and visualising VCF
  ☆28Updated 2 years ago
• Mesh89 / TranSurVeyor
  A transposition caller.
  ☆10Updated 2 years ago
• chrisamiller / copyCat
  a parallel R package for detecting copy-number alterations from short sequencing reads
  ☆23Updated 4 years ago
• umccr / umccrise
  DRAGEN Tumor/Normal workflow post-processing
  ☆24Updated 2 years ago
• HurlesGroupSanger / DeNovoWEST
  ☆23Updated last week
• aganezov / RCK
  RCK: Reconstruction of clone- and haplotype-specific Cancer Karyotypes
  ☆18Updated 5 years ago
• epruesse / ymp
  Flexible omics pipeline
  ☆17Updated last month
• czc / nb_distribution
  novoBreak: local assembly for breakpoint detection in cancer genomes
  ☆25Updated 7 years ago
• bioinform / breakseq2
  BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants
  ☆25Updated 9 years ago
• sigven / cacao
  Callable Cancer Loci - assessment of sequencing coverage for actionable and pathogenic loci in cancer
  ☆21Updated 5 years ago
• aehrc / TRIBES
  Finding cryptic relationships to boost disease gene detection
  ☆12Updated 2 years ago
• favorov / stereogene
  ☆14Updated 3 months ago
• Dowell-Lab / DAStk
  Differential ATAC-seq toolkit
  ☆27Updated last year
• nf-core / deepvariant
  Please consider using/contributing to https://github.com/nf-core/sarek
  ☆41Updated 4 years ago
• polyactis / Accucopy
  Accucopy is a computational method that infers Allele-Specific Copy Number alterations from low-coverage low-purity tumor sequencing data…
  ☆17Updated last year
• bergmanlab / ngs_te_mapper
  Software for detecting transposable element insertions from next-generation sequencing data
  ☆14Updated 4 years ago