Alternatives and similar repositories for gffio

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

• marschall-lab / gaftools
  General purpose utility related to GAF files
  ☆29Updated 2 weeks ago
• kehrlab / PopIns2
  Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs
  ☆24Updated last year
• WHops / NAHRwhals
  R package and wrapper functions for identifying serial structural variations from genome assemblies
  ☆27Updated 11 months ago
• fawaz-dabbaghieh / gfa_subgraphs
  Extracts subgraphs or components from a graph in GFA format
  ☆24Updated 9 months ago
• at-cg / PanAligner
  Long read aligner for cyclic and acyclic pangenome graphs
  ☆39Updated last year
• tlemane / kmdiff
  Differential k-mer analysis
  ☆36Updated last year
• rcedgar / urmap
  URMAP ultra-fast read mapper
  ☆39Updated 5 years ago
• ekg / edyeet
  base-accurate DNA sequence alignments using edlib and mashmap2
  ☆33Updated 4 years ago
• fritzsedlazeck / nibSV
  Kmer based genotyper for short reads.
  ☆23Updated 3 years ago
• lh3 / minisv
  Lightweight mosaic/somatic SV caller for long reads (WIP)
  ☆29Updated 8 months ago
• pierrepeterlongo / back_to_sequences
  ☆44Updated last month
• ekg / gimbricate
  recompute GFA link overlaps
  ☆26Updated 2 years ago
• ldenti / palss
  ☆21Updated 2 months ago
• RolandFaure / Hairsplitter
  Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.
  ☆35Updated 4 months ago
• PacificBiosciences / pbipa
  Improved Phased Assembler
  ☆28Updated 3 years ago
• ACEnglish / kanpig
  Kmer Analysis of Pileups for Genotyping
  ☆32Updated this week
• codialab / GFAffix
  GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
  ☆37Updated 3 months ago
• at-cg / minichain
  Long-read aligner to pangenome graphs
  ☆26Updated last year
• rchikhi / 2022-pangenome-graphs-intro
  ☆28Updated 11 months ago
• wtsi-hpag / scanPAV
  Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
  ☆29Updated 7 years ago
• kehrlab / PopDel
  Population-wide Deletion Calling
  ☆35Updated 4 months ago
• bcgsc / ntLink
  Minimizer-based assembly scaffolding and mapping using long reads
  ☆43Updated 10 months ago
• VGP / vgp-tools
  ☆28Updated 4 months ago
• pangenome / PanSN-spec
  Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes
  ☆39Updated 10 months ago
• at-cg / mm2-plus
  Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)
  ☆33Updated 2 months ago
• ComparativeGenomicsToolkit / hal2vg
  Convert HAL to VG
  ☆22Updated last year
• seryrzu / centroFlye
  An algorithm for centromere assembly using long error-prone reads
  ☆26Updated 4 years ago
• StephenHwang / MEMO
  MEMO: MEM-based pangenome indexing for k-mer queries
  ☆18Updated last year
• mkirsche / Iris
  A module for improving the insertion sequences of structural variant calls
  ☆31Updated 4 years ago
• Parsoa / SVDSS
  Improved structural variant discovery in accurate long reads using sample-specific strings (SFS)
  ☆44Updated 2 months ago