Alternatives and similar repositories for gfabase

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

• pangenome / maffer
  extract MSAs from genome variation graphs
  ☆34Updated 5 years ago
• codialab / GFAffix
  GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
  ☆37Updated 8 months ago
• ekg / edyeet
  base-accurate DNA sequence alignments using edlib and mashmap2
  ☆32Updated 4 years ago
• pangenome / gafpack
  convert variation graph alignments to coverage maps over nodes
  ☆27Updated 2 weeks ago
• pangenome / pgge
  the pangenome graph evaluator
  ☆29Updated 4 years ago
• marschall-lab / gaftools
  General purpose utility related to GAF files
  ☆29Updated last week
• ekg / gimbricate
  recompute GFA link overlaps
  ☆25Updated 3 years ago
• at-cg / PanAligner
  Long read aligner for cyclic and acyclic pangenome graphs
  ☆40Updated 2 years ago
• mkirsche / Iris
  A module for improving the insertion sequences of structural variant calls
  ☆33Updated 4 years ago
• benedictpaten / marginPhase
  ☆35Updated 5 years ago
• alshai / levioSAM
  Lift-over alignments from variant-aware references
  ☆34Updated 2 years ago
• MoinSebi / gretl
  Statistics and analysis for variation graphs
  ☆48Updated last year
• vgteam / libbdsg
  Optimized sequence graph implementations for graph genomics
  ☆34Updated this week
• WHops / NAHRwhals
  R package and wrapper functions for identifying serial structural variations from genome assemblies
  ☆29Updated last year
• edawson / gfakluge
  A C++ library and utilities for manipulating the Graphical Fragment Assembly format.
  ☆55Updated 3 years ago
• lh3 / pubLRasm
  ☆17Updated 5 years ago
• tlemane / kmdiff
  Differential k-mer analysis
  ☆39Updated 2 years ago
• rchikhi / 2022-pangenome-graphs-intro
  ☆28Updated last year
• pangenome / pgvf-spec
  Pangenome Graph Variation Format (PGVF)
  ☆19Updated 5 years ago
• fritzsedlazeck / SVCollector
  Method to optimally select samples for validation and resequencing
  ☆30Updated 4 years ago
• pangenome / PanSN-spec
  Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes
  ☆44Updated last year
• fritzsedlazeck / nibSV
  Kmer based genotyper for short reads.
  ☆23Updated 4 years ago
• pangenome / vcfbub
  use variant nesting information to flter overlapping sites from vg deconstruct output
  ☆31Updated 7 months ago
• at-cg / minichain
  Long-read aligner to pangenome graphs
  ☆29Updated last year
• vpc-ccg / sedef
  Identification of segmental duplications in the genome
  ☆27Updated 3 years ago
• pangenome / smoothxg
  linearize and simplify variation graphs using blocked partial order alignment
  ☆60Updated 6 months ago
• seryrzu / centroFlye
  An algorithm for centromere assembly using long error-prone reads
  ☆25Updated 4 years ago
• PacificBiosciences / portello
  Transfer HiFi read mappings from their own assembly contigs to a standard reference
  ☆29Updated last month
• iqbal-lab-org / make_prg
  Code to create a PRG from a Multiple Sequence Alignment file
  ☆25Updated 4 months ago
• ablab / stringdecomposer
  Tool for decomposition centromeric assemblies and long reads into monomers
  ☆37Updated 3 years ago