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…
  ☆145Updated 6 months ago
• DecodeGenetics / graphtyper
  Population-scale genotyping using pangenome graphs
  ☆195Updated last year
• parklab / bamsnap
  ☆122Updated 5 months ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆152Updated last month
• dnanexus-archive / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆103Updated 5 years ago
• NAL-i5K / GFF3toolkit
  Python programs for processing GFF3 files
  ☆102Updated last month
• Oshlack / Corset
  Software for clustering de novo assembled transcripts and counting overlapping reads
  ☆76Updated 3 years ago
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆156Updated 3 years ago
• wurmlab / flo
  Same species annotation lift over pipeline.
  ☆98Updated 2 years ago
• broadinstitute / gatk-docs
  Documentation archive for GATK tools and workflows
  ☆92Updated 6 years ago
• dentearl / mafTools
  Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.
  ☆109Updated 3 years ago
• Illumina / paragraph
  Graph realignment tools for structural variants
  ☆165Updated 3 years ago
• bergmanlab / mcclintock
  Meta-pipeline to identify transposable element insertions using next generation sequencing data
  ☆105Updated 7 months ago
• 10XGenomics / supernova
  10x Genomics Linked-Read Diploid De Novo Assembler
  ☆65Updated 7 years ago
• PacificBiosciences / pb-assembly
  PacBio Assembly Tool Suite: Reads in ⇨ Assembly out
  ☆118Updated 5 years ago
• compbiocore / VariantVisualization.jl
  Julia package powering VIVA, our tool for visualization of genomic variation data. Manual:
  ☆87Updated 2 years ago
• MikkelSchubert / adapterremoval
  AdapterRemoval v2 - rapid adapter trimming, identification, and read merging
  ☆113Updated this week
• ComparativeGenomicsToolkit / hal
  Hierarchical Alignment Format
  ☆174Updated last month
• zstephens / neat-genreads
  NEAT read simulation tools
  ☆101Updated 3 years ago
• jstjohn / SeqPrep
  Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
  ☆145Updated 9 years ago
• brentp / duphold
  don't get DUP'ed or DEL'ed by your putative SVs.
  ☆107Updated 5 years ago
• nanoporetech / pipeline-structural-variation
  Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
  ☆115Updated 4 years ago
• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆160Updated 10 months ago
• odelaneau / shapeit4
  Segmented HAPlotype Estimation and Imputation Tool
  ☆98Updated 2 years ago
• alastair-droop / fqtools
  An efficient FASTQ manipulation suite
  ☆138Updated 5 years ago
• secastel / phaser
  phasing and Allele Specific Expression from RNA-seq
  ☆117Updated last year
• PacificBiosciences / DevNet
  The DevNet project on github stores the PacBio DevNet website.
  ☆116Updated 7 years ago
• mroosmalen / nanosv
  SV caller for nanopore data
  ☆92Updated 5 years ago
• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆120Updated 3 months ago
• cpockrandt / genmap
  GenMap - Fast and Exact Computation of Genome Mappability
  ☆113Updated last year