Alternatives and similar repositories for pafcheck

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

• StephenHwang / MEMO
  MEMO: MEM-based pangenome indexing for k-mer queries
  ☆18Updated 11 months ago
• T2T-apes / ape_pangenome
  pangenome analyses for complete genomes of great apes (and gibbon)
  ☆17Updated 7 months ago
• marbl / training
  Genome Assembly 102
  ☆13Updated last month
• mobinasri / secphase
  Phasing reads with secondary alignments
  ☆18Updated 6 months ago
• ASLeonard / pandrawer
  Everything but the kitchen sink
  ☆11Updated 4 months ago
• jmonlong / manu-vggafannot
  Efficient indexing and querying of annotations in a pangenome graph
  ☆9Updated 7 months ago
• ekg / fastix
  Prefix-renaming FASTA records really fast.
  ☆17Updated 11 months ago
• magspho / hifieval
  a tool to evaluate long-read error correction mainly with PacBio High-Fidelity Reads (HiFi reads).
  ☆21Updated last year
• fawaz-dabbaghieh / gfa_subgraphs
  Extracts subgraphs or components from a graph in GFA format
  ☆23Updated 6 months ago
• pdishuck / GAVISUNK
  Genome Assembly Validation via Inter-SUNK distances in ONT reads
  ☆12Updated 2 years ago
• pangenome / vcfbub
  use variant nesting information to flter overlapping sites from vg deconstruct output
  ☆26Updated 11 months ago
• Maize-Genetics-and-Genomics-Database / PanEffect
  PanEffect is a JavaScript framework to explore variant effects across a pangenome. The tool has two views that allows a user to (1) expl…
  ☆13Updated last year
• Adamtaranto / TIRmite
  Map TIR-pHMM models to genomic sequences for annotation of MITES and complete DNA-Transposons.
  ☆10Updated last month
• Walfred-MA / Ctyper
  Genotyping of copy number sensitive allele-specific haplotypes
  ☆15Updated last week
• TravisWheelerLab / BATH
  Better Alignments with Translated HMMER
  ☆21Updated last week
• davidebolo1993 / cosigt
  ☆19Updated last week
• lh3 / TRF-mod
  Tandem Repeats Finder: a program to analyze DNA sequences
  ☆15Updated 2 years ago
• chfi / gfainject
  ☆16Updated 2 years ago
• rlorigro / simple-dotplot
  Very simple and configurable all-in-one dotplot program
  ☆13Updated 2 years ago
• MoinSebi / gfa2bin
  ☆24Updated 6 months ago
• cumtr / PG-SCUnK
  PG-SCUnK mesure quality of Pan-Genome Graphs using Single Copy and Universal k-mers
  ☆18Updated last week
• makovalab-psu / T2T_primate_XY
  ☆12Updated 11 months ago
• GeneDx / pgr-tk-notebooks
  Jupyter Notebooks Using PGR-TK for various human pangenome analysis tasks
  ☆15Updated 2 years ago
• ComparativeGenomicsToolkit / hal2vg
  Convert HAL to VG
  ☆22Updated 9 months ago
• DessimozLab / edgehog
  Infering ancestral synteny with hierarchical orthologous groups
  ☆14Updated last week
• lrobidou / KFC
  ☆18Updated 3 months ago
• at-cg / PanAligner
  Long read aligner for cyclic and acyclic pangenome graphs
  ☆36Updated last year
• richarddurbin / syng
  syncmer graphs, and perhaps other sorts of sequence graphs
  ☆20Updated 2 months ago
• AndreaGuarracino / 1000G-ONT-F100-PGGB
  PanGenome Graph Building with the first 100 assemblies from the 1000G ONT Sequencing Consortium
  ☆12Updated 2 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