Alternatives and similar repositories for pancat

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

• ShunOuchi / GreenHill
  De novo chromosome-level scaffolding and phasing tool using Hi-C
  ☆29Updated 7 months ago
• WHops / NAHRwhals
  R package and wrapper functions for identifying serial structural variations from genome assemblies
  ☆27Updated last year
• aljpetri / isONform
  De novo construction of isoforms from long-read data
  ☆34Updated 4 months ago
• human-pangenomics / hprc-tutorials
  ☆18Updated last year
• gatech-genemark / GeneMark-ETP
  GeneMark-ETP: gene finding in eukaryotic genomes supported by transcriptome sequencing and protein homology
  ☆25Updated 6 months ago
• marschall-lab / gaftools
  General purpose utility related to GAF files
  ☆29Updated this week
• at-cg / mm2-plus
  Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)
  ☆35Updated 4 months ago
• AdamCicherski / AlfaPang
  AlfaPang builds pangenome graphs without alignments or references.
  ☆13Updated 4 months ago
• RolandFaure / Hairsplitter
  Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.
  ☆35Updated 6 months ago
• fawaz-dabbaghieh / bubble_gun
  ☆40Updated 2 months ago
• nf-core / genomeannotator
  Pipeline for the identification of (coding) gene structures in draft genomes.
  ☆30Updated last year
• codialab / GFAffix
  GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
  ☆36Updated 5 months ago
• tprodanov / locityper
  Targeted genotyper for complex polymorphic genes
  ☆29Updated this week
• marbl / training
  Genome Assembly 102
  ☆14Updated 6 months ago
• pierrepeterlongo / back_to_sequences
  ☆45Updated 2 weeks ago
• lemene / PECAT
  PECAT, a phased error correct and assembly tool
  ☆54Updated 3 months ago
• cumtr / PG-SCUnK
  PG-SCUnK mesure quality of Pan-Genome Graphs using Single Copy and Universal k-mers
  ☆19Updated last month
• w-gao / pgv
  A web-based, interactive pangenome visualization tool
  ☆21Updated 2 years ago
• a-ludi / dentist
  Close assembly gaps using long-reads at high accuracy.
  ☆49Updated last year
• at-cg / RAFT
  ☆28Updated last year
• pangenome / gafpack
  convert variation graph alignments to coverage maps over nodes
  ☆26Updated last week
• at-cg / minichain
  Long-read aligner to pangenome graphs
  ☆27Updated last year
• ComparativeGenomicsToolkit / taffy
  This is a library C/Python/CLI for working with TAF (.taf,.taf.gz) and MAF (.maf) alignment files
  ☆29Updated 2 months ago
• at-cg / PanAligner
  Long read aligner for cyclic and acyclic pangenome graphs
  ☆39Updated last year
• MoinSebi / gfa2bin
  ☆25Updated 2 months ago
• pangenome / maffer
  extract MSAs from genome variation graphs
  ☆33Updated 5 years ago
• ACEnglish / kanpig
  Kmer Analysis of Pileups for Genotyping
  ☆32Updated 2 weeks ago
• bcgsc / ntLink
  Minimizer-based assembly scaffolding and mapping using long reads
  ☆43Updated last year
• sanger-tol / PretextMap
  Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.
  ☆22Updated 2 weeks ago
• asylvz / SVarp
  Phased structural variant discovery in pangenomes
  ☆37Updated last year