Alternatives and similar repositories for VCF-kit

Users that are interested in VCF-kit are comparing it to the libraries listed below

• wurmlab / flo
  Same species annotation lift over pipeline.
  ☆97Updated last year
• parklab / bamsnap
  ☆122Updated 7 months ago
• bergmanlab / mcclintock
  Meta-pipeline to identify transposable element insertions using next generation sequencing data
  ☆100Updated 3 weeks ago
• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆153Updated 4 months ago
• MariaNattestad / Assemblytics
  Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference gen…
  ☆141Updated 7 months ago
• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆118Updated 2 months ago
• nanoporetech / pipeline-structural-variation
  Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
  ☆114Updated 3 years ago
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆173Updated 4 years ago
• brentp / duphold
  don't get DUP'ed or DEL'ed by your putative SVs.
  ☆106Updated 4 years ago
• PacificBiosciences / pb-assembly
  PacBio Assembly Tool Suite: Reads in ⇨ Assembly out
  ☆118Updated 4 years ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆150Updated 4 months ago
• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆185Updated last year
• Griffan / VerifyBamID
  VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
  ☆97Updated last year
• hall-lab / svtyper
  Bayesian genotyper for structural variants
  ☆134Updated 4 years ago
• JimWhiting91 / genotype_plot
  A set of functions to visualise genotypes based on a VCF
  ☆86Updated 3 years ago
• mkirsche / Jasmine
  Jasmine: SV Merging Across Samples
  ☆216Updated 6 months ago
• EichlerLab / pav
  Phased assembly variant caller
  ☆120Updated 6 months ago
• mroosmalen / nanosv
  SV caller for nanopore data
  ☆91Updated 5 years ago
• compbiocore / VariantVisualization.jl
  Julia package powering VIVA, our tool for visualization of genomic variation data. Manual:
  ☆86Updated last year
• dnanexus-archive / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆102Updated 4 years ago
• sujaikumar / assemblage
  Tools for working with second gen assemblies, fasta sequences, etc
  ☆93Updated 8 years ago
• gencorefacility / variant-calling-pipeline-gatk4
  Variant Calling Pipeline Using GATK4 and Nextflow
  ☆56Updated 2 years ago
• moiexpositoalonsolab / grenepipe
  A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - fo…
  ☆101Updated last week
• nanoporetech / pychopper
  A tool to identify, orient, trim and rescue full length cDNA reads
  ☆82Updated 2 years ago
• alastair-droop / fqtools
  An efficient FASTQ manipulation suite
  ☆137Updated 5 years ago
• Oshlack / Corset
  Software for clustering de novo assembled transcripts and counting overlapping reads
  ☆71Updated 3 years ago
• voichek / kmersGWAS
  A library for running k-mers based GWAS
  ☆109Updated 7 months ago
• nhansen / SVanalyzer
  Tools for the analysis of structural variation in genomes
  ☆79Updated last year
• geocarvalho / sv-cnv-studies
  Relevant papers for CNV and SV approaches
  ☆94Updated 7 months ago
• rrwick / Deepbinner
  a signal-level demultiplexer for Oxford Nanopore reads
  ☆126Updated 4 years ago