Alternatives and similar repositories for graphtyper

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

• AndersenLab / VCF-kit
  VCF-kit: Assorted utilities for the variant call format
  ☆131Updated 4 months ago
• hall-lab / svtools
  Tools for processing and analyzing structural variants.
  ☆154Updated 3 years ago
• mkirsche / Jasmine
  Jasmine: SV Merging Across Samples
  ☆230Updated 10 months ago
• marbl / SALSA
  SALSA: A tool to scaffold long read assemblies with Hi-C data
  ☆187Updated last year
• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆160Updated 8 months ago
• hall-lab / svtyper
  Bayesian genotyper for structural variants
  ☆136Updated 4 years ago
• Illumina / paragraph
  Graph realignment tools for structural variants
  ☆164Updated 2 years ago
• parklab / bamsnap
  ☆123Updated 3 months ago
• vibansal / HapCUT2
  software tools for haplotype assembly from sequence data
  ☆223Updated 9 months ago
• adamewing / methylartist
  Tools for plotting methylation data in various ways
  ☆164Updated this week
• zstephens / neat-genreads
  NEAT read simulation tools
  ☆101Updated 3 years ago
• Illumina / ExpansionHunter
  A tool for estimating repeat sizes
  ☆198Updated last year
• GenomeRIK / tama
  Transcriptome Annotation by Modular Algorithms (for long read RNA sequencing data)
  ☆162Updated 2 years ago
• PacificBiosciences / ccs
  CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)
  ☆125Updated last year
• nanoporetech / pipeline-structural-variation
  Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
  ☆114Updated 4 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆249Updated 2 months ago
• ComparativeGenomicsToolkit / hal
  Hierarchical Alignment Format
  ☆173Updated 2 months ago
• brentp / smoove
  structural variant calling and genotyping with existing tools, but, smoothly.
  ☆259Updated last year
• broadinstitute / long-read-pipelines
  Long read production pipelines
  ☆150Updated last week
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆151Updated 3 weeks ago
• nanoporetech / pipeline-transcriptome-de
  Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
  ☆108Updated 2 years ago
• dnanexus-rnd / GLnexus
  Scalable gVCF merging and joint variant calling for population sequencing projects
  ☆171Updated last year
• nanoporetech / pychopper
  A tool to identify, orient, trim and rescue full length cDNA reads
  ☆83Updated 3 years ago
• Griffan / VerifyBamID
  VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
  ☆99Updated last year
• jstjohn / SeqPrep
  Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
  ☆145Updated 9 years 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…
  ☆146Updated 4 months ago
• human-pangenomics / hpp_pangenome_resources
  ☆124Updated 2 years ago
• atks / vt
  A tool set for short variant discovery in genetic sequence data.
  ☆202Updated 4 years ago
• gpertea / gffcompare
  classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
  ☆250Updated 4 months ago
• lh3 / gfatools
  Tools for manipulating sequence graphs in the GFA and rGFA formats
  ☆239Updated last year