Alternatives and similar repositories for palss:

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

• WHops / NAHRwhals
  R package and wrapper functions for identifying serial structural variations from genome assemblies
  ☆29Updated 7 months ago
• marschall-lab / gaftools
  General purpose utility related to GAF files
  ☆24Updated 3 weeks ago
• StephenHwang / MEMO
  MEMO: MEM-based pangenome indexing for k-mer queries
  ☆18Updated 10 months ago
• lh3 / gffio
  ☆32Updated 2 years ago
• fawaz-dabbaghieh / gfa_subgraphs
  Extracts subgraphs or components from a graph in GFA format
  ☆23Updated 5 months ago
• w-gao / pgv
  A web-based, interactive pangenome visualization tool
  ☆21Updated 2 years ago
• davidebolo1993 / cosigt
  ☆17Updated last week
• chfi / gfainject
  ☆15Updated last year
• ekg / gimbricate
  recompute GFA link overlaps
  ☆25Updated 2 years ago
• marbl / training
  Genome Assembly 102
  ☆14Updated 2 weeks ago
• ekg / pafcheck
  PAF (pairwise alignment format) validator based on extended CIGAR strings
  ☆14Updated 7 months ago
• fritzsedlazeck / nibSV
  Kmer based genotyper for short reads.
  ☆23Updated 3 years ago
• rchikhi / 2022-pangenome-graphs-intro
  ☆28Updated 7 months ago
• magspho / hifieval
  a tool to evaluate long-read error correction mainly with PacBio High-Fidelity Reads (HiFi reads).
  ☆21Updated last year
• lh3 / minisv
  Lightweight mosaic/somatic SV caller for long reads (WIP)
  ☆28Updated 5 months ago
• RolandFaure / Hairsplitter
  Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.
  ☆34Updated 2 weeks ago
• pangenome / vcfbub
  use variant nesting information to flter overlapping sites from vg deconstruct output
  ☆26Updated 10 months ago
• ACEnglish / kanpig
  Kmer Analysis of Pileups for Genotyping
  ☆29Updated 3 weeks ago
• ASLeonard / pandrawer
  Everything but the kitchen sink
  ☆11Updated 3 months ago
• tprodanov / locityper
  Targeted genotyper for complex polymorphic genes
  ☆20Updated this week
• pdishuck / GAVISUNK
  Genome Assembly Validation via Inter-SUNK distances in ONT reads
  ☆12Updated 2 years ago
• T2T-apes / ape_pangenome
  pangenome analyses for complete genomes of great apes (and gibbon)
  ☆17Updated 6 months ago
• MoinSebi / gfa2bin
  ☆21Updated 5 months ago
• ekg / fastix
  Prefix-renaming FASTA records really fast.
  ☆17Updated 10 months ago
• jmonlong / pangenome-evaluation
  Pipeline to evaluate pangenomes, e.g. from the variation it contains or how well reads map
  ☆10Updated 3 years ago
• human-pangenomics / hprc-tutorials
  ☆17Updated last year
• kehrlab / PopIns2
  Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs
  ☆24Updated last year
• GTPB / CPANG22
  Computational Pangenomics
  ☆17Updated 2 years ago
• lh3 / TRF-mod
  Tandem Repeats Finder: a program to analyze DNA sequences
  ☆14Updated 2 years ago
• pangenome / PanSN-spec
  Pangenome Sequence Naming: a backwards-compatible hack to simplify the identification of samples and haplotypes in pangenomes
  ☆38Updated 6 months ago