Alternatives and similar repositories for VCF-kit

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

• MariaNattestad / Assemblytics
  Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference gen…
  ☆142Updated 3 weeks ago
• nanoporetech / pipeline-structural-variation
  Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
  ☆114Updated 3 years ago
• DecodeGenetics / graphtyper
  Population-scale genotyping using pangenome graphs
  ☆188Updated 7 months ago
• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆155Updated 5 months ago
• parklab / bamsnap
  ☆123Updated last week
• dnanexus-archive / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆102Updated 4 years ago
• ComparativeGenomicsToolkit / hal
  Hierarchical Alignment Format
  ☆170Updated 7 months ago
• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆188Updated last year
• broadinstitute / gatk-docs
  Documentation archive for GATK tools and workflows
  ☆88Updated 5 years ago
• adamewing / methylartist
  Tools for plotting methylation data in various ways
  ☆159Updated last week
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆149Updated 3 weeks ago
• MikkelSchubert / adapterremoval
  AdapterRemoval v2 - rapid adapter trimming, identification, and read merging
  ☆113Updated 2 months ago
• Oshlack / Corset
  Software for clustering de novo assembled transcripts and counting overlapping reads
  ☆72Updated 3 years ago
• Illumina / paragraph
  Graph realignment tools for structural variants
  ☆159Updated 2 years ago
• jstjohn / SeqPrep
  Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
  ☆144Updated 8 years ago
• odelaneau / shapeit4
  Segmented HAPlotype Estimation and Imputation Tool
  ☆95Updated last year
• hall-lab / svtyper
  Bayesian genotyper for structural variants
  ☆134Updated 4 years ago
• NAL-i5K / GFF3toolkit
  Python programs for processing GFF3 files
  ☆98Updated last year
• bergmanlab / mcclintock
  Meta-pipeline to identify transposable element insertions using next generation sequencing data
  ☆103Updated 2 months ago
• alastair-droop / fqtools
  An efficient FASTQ manipulation suite
  ☆138Updated 5 years ago
• wdecoster / methplotlib
  Plotting tools for nanopore methylation data
  ☆93Updated last week
• 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 2 years ago
• brentp / duphold
  don't get DUP'ed or DEL'ed by your putative SVs.
  ☆106Updated 4 years ago
• zstephens / neat-genreads
  NEAT read simulation tools
  ☆98Updated 3 years ago
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆154Updated 3 years ago
• mkirsche / Jasmine
  Jasmine: SV Merging Across Samples
  ☆219Updated 7 months ago
• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆118Updated 3 months ago
• moiexpositoalonsolab / grenepipe
  A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles - fo…
  ☆103Updated last month
• alimanfoo / pysamstats
  A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …
  ☆194Updated last week