Alternatives and similar repositories for PanPipes

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

• fritzsedlazeck / sge_mummer
  Scripts to split reference and run mummer in parallel on an SGE cluster
  ☆11Updated 9 years ago
• fawaz-dabbaghieh / gfa_subgraphs
  Extracts subgraphs or components from a graph in GFA format
  ☆24Updated last year
• nextgenusfs / redmask
  Genome assembly soft-masking using Red (REpeat Detector)
  ☆18Updated 7 years ago
• ekg / fastix
  Prefix-renaming FASTA records really fast.
  ☆17Updated last year
• mikolmogorov / maf2synteny
  A tool for recovering synteny blocks from multiple alignment
  ☆32Updated 4 years ago
• ekg / pafplot
  base-level dotplots from PAF alignments
  ☆30Updated 4 months ago
• SandraLouise / SVJedi-graph
  SV genotyper for long reads with a variation graph
  ☆15Updated 5 months ago
• PacificBiosciences / pbipa
  Improved Phased Assembler
  ☆28Updated 3 years ago
• atifrahman / SWALO
  Scaffolding with assembly likelihood optimization
  ☆21Updated 5 years ago
• MoinSebi / gfa2bin
  ☆28Updated 5 months ago
• WHops / NAHRwhals
  R package and wrapper functions for identifying serial structural variations from genome assemblies
  ☆29Updated last year
• reubwn / collinearity
  scripts to parse and analyse MCScanX collinearity output
  ☆33Updated 5 years ago
• davidebolo1993 / cosigt
  COsine SImilarity-based Genotyper using pangenomes
  ☆25Updated last week
• jbelyeu / PlotCritic
  Python deployment tool for bespoke image curation projects, oriented toward scientific projects. Please cite https://academic.oup.com/gig…
  ☆13Updated 3 years ago
• isugifNF / polishCLR
  A nextflow pipeline for polishing CLR assemblies
  ☆18Updated 2 years ago
• seryrzu / centroFlye
  An algorithm for centromere assembly using long error-prone reads
  ☆25Updated 4 years ago
• tolkit / fasta_windows
  A Rust implementation of sliding window stats over fastas.
  ☆15Updated 4 months ago
• lpryszcz / pyScaf
  Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.
  ☆24Updated 7 years ago
• cumtr / PG-SCUnK
  PG-SCUnK mesure quality of Pan-Genome Graphs using Single Copy and Universal k-mers
  ☆23Updated 2 months ago
• nadegeguiglielmoni / GraphUnzip
  Unzip assembly graphs with Hi-C data and/or long reads.
  ☆27Updated last year
• sanger-tol / PretextMap
  Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.
  ☆24Updated last week
• vpc-ccg / sedef
  Identification of segmental duplications in the genome
  ☆27Updated 3 years ago
• OmarOakheart / nPhase
  Ploidy agnostic phasing pipeline and algorithm
  ☆49Updated 2 years ago
• RolandFaure / Hairsplitter
  Software that separates very close sequences that have been collapsed during assembly. Uses only long reads.
  ☆35Updated 9 months ago
• mahulchak / mscaffolder
  A comparative genome scaffolding tool
  ☆16Updated 7 years ago
• ablab / stringdecomposer
  Tool for decomposition centromeric assemblies and long reads into monomers
  ☆37Updated 3 years ago
• ekg / gimbricate
  recompute GFA link overlaps
  ☆25Updated 3 years ago
• jydu / maffilter
  The MafFilter genome alignment processor
  ☆19Updated 3 weeks ago
• AndreaGuarracino / paf2chain
  convert PAF format to CHAIN format
  ☆34Updated 8 months ago
• pangenome / vcfbub
  use variant nesting information to flter overlapping sites from vg deconstruct output
  ☆31Updated 7 months ago