Alternatives and similar repositories for shapeit4

Users that are interested in shapeit4 are comparing it to the libraries listed below

• szpiech / selscan
  Haplotype based scans for selection
  ☆136Updated last month
• dentearl / mafTools
  Bioinformatics tools for dealing with Multiple Alignment Format (MAF) files.
  ☆109Updated 3 years ago
• parklab / bamsnap
  ☆123Updated 4 months ago
• dnanexus-archive / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆103Updated 5 years ago
• wurmlab / flo
  Same species annotation lift over pipeline.
  ☆98Updated 2 years ago
• mroosmalen / nanosv
  SV caller for nanopore data
  ☆92Updated 5 years ago
• JimWhiting91 / genotype_plot
  A set of functions to visualise genotypes based on a VCF
  ☆87Updated 3 years ago
• Illumina / paragraph
  Graph realignment tools for structural variants
  ☆164Updated 3 years ago
• tobiasrausch / wally
  Wally: Visualization of aligned sequencing reads and contigs
  ☆120Updated 2 months ago
• thlee / SNPhylo
  A pipeline to generate a phylogenetic tree from huge SNP data
  ☆92Updated last year
• rwdavies / STITCH
  STITCH - Sequencing To Imputation Through Constructing Haplotypes
  ☆85Updated last month
• AndersenLab / VCF-kit
  VCF-kit: Assorted utilities for the variant call format
  ☆132Updated 4 months ago
• zstephens / neat-genreads
  NEAT read simulation tools
  ☆101Updated 3 years ago
• Illumina / ExpansionHunterDenovo
  A suite of tools for detecting expansions of short tandem repeats
  ☆83Updated 2 years ago
• brentp / duphold
  don't get DUP'ed or DEL'ed by your putative SVs.
  ☆107Updated 4 years ago
• kcleal / dysgu
  Toolkit for calling structural variants using short or long reads
  ☆113Updated 2 months ago
• bergmanlab / mcclintock
  Meta-pipeline to identify transposable element insertions using next generation sequencing data
  ☆105Updated 6 months ago
• milkschen / leviosam2
  Fast and accurate coordinate conversion between assemblies
  ☆117Updated 2 months ago
• EichlerLab / pav
  Phased assembly variant caller
  ☆129Updated last year
• voichek / kmersGWAS
  A library for running k-mers based GWAS
  ☆122Updated last year
• ChaissonLab / LRA
  Long read aligner
  ☆115Updated 2 years ago
• CSB5 / lofreq
  LoFreq Star: Sensitive variant calling from sequencing data
  ☆108Updated last month
• odelaneau / shapeit5
  Segmented HAPlotype Estimation and Imputation Tool
  ☆91Updated this week
• hall-lab / svtyper
  Bayesian genotyper for structural variants
  ☆136Updated 4 years ago
• mozack / abra2
  ABRA2
  ☆95Updated 3 years ago
• walaj / VariantBam
  Filtering and profiling of next-generational sequencing data using region-specific rules
  ☆79Updated 2 years ago
• twolinin / longphase
  ☆119Updated 3 weeks ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆151Updated last week
• sujaikumar / assemblage
  Tools for working with second gen assemblies, fasta sequences, etc
  ☆93Updated 9 years ago
• PacificBiosciences / trgt
  Tandem repeat genotyping and visualization from PacBio HiFi data
  ☆129Updated 3 weeks ago