Alternatives and similar repositories for tomahawk

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

• lh3 / htsbox
  My experimental tools on top of htslib. NOT OFFICIAL!!!
  ☆58Updated 3 months ago
• atifrahman / HAWK
  Hitting associations with k-mers
  ☆44Updated 3 years ago
• ekg / bamaddrg
  adds sample names and read-group (RG) tags to BAM alignments
  ☆51Updated 5 years ago
• lh3 / etrf
  Exact Tandem Repeat Finder (not a TRF replacement)
  ☆51Updated 6 years ago
• bioinformatics-centre / BayesTyper
  A method for variant graph genotyping based on exact alignment of k-mers
  ☆87Updated 6 years ago
• brwnj / covviz
  Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata
  ☆58Updated 3 years ago
• sestaton / Transposome
  A toolkit for annotation of transposable element families from unassembled sequence reads
  ☆31Updated last week
• Oshlack / STRetch
  Method for detecting STR expansions from short-read sequencing data
  ☆63Updated 4 years ago
• bcgsc / ntCard
  Estimating k-mer coverage histogram of genomics data
  ☆77Updated 2 years ago
• PacificBiosciences / svpack
  Structural variant (SV) analysis tools
  ☆39Updated last year
• aquaskyline / LRSIM
  10x Genomics Reads Simulator
  ☆46Updated 2 years ago
• dillonl / graphite
  Graphite - Graph-based variant adjudication
  ☆28Updated 4 years ago
• jandrewrfarrell / RUFUS
  RUFUS k-mer based genomic variant detection
  ☆54Updated last month
• lbcb-sci / ra
  Assembler for raw de novo genome assembly of long uncorrected reads.
  ☆36Updated 6 years ago
• tk2 / RetroSeq
  RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference…
  ☆67Updated 3 years ago
• jbelyeu / SV-plaudit
  Pipeline for structural variant image curation and analysis.
  ☆49Updated 4 years ago
• pachterlab / metakallisto
  Using kallisto for metagenomic analysis
  ☆49Updated 8 years ago
• hall-lab / sv-pipeline
  Pipeline for structural variation detection in cohorts
  ☆52Updated 4 years ago
• mskilab-org / gGnome
  R API for browsing, analyzing, and manipulating reference-aligned genome graphs in a GenomicRanges framework
  ☆41Updated 2 weeks ago
• ksahlin / ultra
  Long-read splice alignment with high accuracy
  ☆64Updated last year
• grocsvs / grocsvs
  Genome-wide reconstruction of complex structural variants
  ☆39Updated 3 years ago
• benedictpaten / marginAlign
  UCSC Nanopore
  ☆44Updated 6 years ago
• lh3 / sgdp-fermi
  FermiKit small variant calls for public SGDP samples
  ☆17Updated 9 years ago
• kamimrcht / REINDEER
  REINDEER REad Index for abuNDancE quERy
  ☆56Updated 5 months ago
• Oshlack / Lace
  Building SuperTranscripts: A linear representation of transcriptome data
  ☆68Updated 4 years ago
• schmeing / ReSeq
  More realistic simulator for genomic DNA sequences from Illumina machines that achieves a similar k-mer spectrum as the original
  ☆51Updated 3 years ago
• jkbonfield / crumble
  Exploration of controlled loss of quality values for compressing CRAM files
  ☆36Updated 2 years ago
• TheJacksonLaboratory / SVE
  ☆51Updated 6 years ago
• conchoecia / pauvre
  Pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads.
  ☆54Updated last year
• kevlar-dev / kevlar
  Reference-free variant discovery in large eukaryotic genomes
  ☆41Updated 4 years ago