Alternatives and similar repositories for pipelines

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

• DessimozLab / OMAnnotator
  Consensus genome annotation using OMA
  ☆27Updated 4 months ago
• mobinasri / secphase
  Phasing reads with secondary alignments
  ☆21Updated 11 months ago
• isugifNF / polishCLR
  A nextflow pipeline for polishing CLR assemblies
  ☆18Updated 2 years ago
• gtrichard / mummer-ggplot
  Nucmer from Mummer3 followed by ggplot for nicer and more customisable genome alignment plots.
  ☆11Updated 4 years ago
• yangli557 / AnnoSINE
  SINE annotation tool for plant genomes
  ☆18Updated last year
• WarrenLab / chicken-pangenome-paper
  Scripts used to perform analyses in Rice et al. (2023)
  ☆15Updated last year
• davidebolo1993 / cosigt
  COsine SImilarity-based Genotyper using pangenomes
  ☆23Updated last week
• institut-de-genomique / HAPO-G
  Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.
  ☆25Updated 3 weeks ago
• mikolmogorov / maf2synteny
  A tool for recovering synteny blocks from multiple alignment
  ☆32Updated 4 years ago
• DessimozLab / edgehog
  Infering ancestral synteny with hierarchical orthologous groups
  ☆35Updated last month
• esolares / HapSolo
  Reduction of Althaps and Duplicate Contigs for Improved Hi-C Scaffolding
  ☆20Updated 8 months ago
• Wenfei-Xian / TIPP
  Telomere local assembly, Improved whole genome polish, and Plastid assembly
  ☆21Updated 6 months ago
• phasegenomics / matlock
  Simple tools for working with Hi-C data
  ☆18Updated 6 years ago
• marbl / training
  Genome Assembly 102
  ☆14Updated 6 months ago
• HuiyangYu / TGSFilter
  TGSFilter: An ultra-fast and efficient tool for long reads filtering and trimming
  ☆25Updated last year
• wtsi-hpag / scanPAV
  Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
  ☆29Updated 7 years ago
• at-cg / RAFT
  ☆28Updated last year
• dfguan / pin_hic
  A Hi-C scaffolding method
  ☆22Updated 3 years ago
• logsdon-lab / CenMAP
  Centromere mapping and annotation pipeline
  ☆16Updated 2 weeks ago
• gf777 / mitoVGP
  The Vertebrate Genomes Project Mitogenome Assembly Pipeline
  ☆19Updated 2 years ago
• legumeinfo / pandagma
  Generate pan-gene sets, given a collection of genome assemblies and corresponding gene models.
  ☆17Updated 3 months ago
• esrice / PBJelly
  a fork of the gap-closing pipeline PBJelly
  ☆15Updated 6 years ago
• mcsimenc / PhyLTR
  Phylogenetic Analysis of Long Terminal Repeat Retrotransposons
  ☆18Updated 3 years ago
• cumtr / PG-SCUnK
  PG-SCUnK mesure quality of Pan-Genome Graphs using Single Copy and Universal k-mers
  ☆19Updated this week
• magspho / hifieval
  a tool to evaluate long-read error correction mainly with PacBio High-Fidelity Reads (HiFi reads).
  ☆21Updated last year
• jnarayan81 / parallelLastz
  parallelLastz: Running Lastz in parallel
  ☆17Updated last year
• Adamtaranto / TRF2GFF
  Convert Tandem Repeat Finder dat file output into gff3 format
  ☆28Updated last week
• Adamtaranto / TIRmite
  Map TIR-pHMM models to genomic sequences for annotation of MITES and complete DNA-Transposons.
  ☆10Updated 3 months ago
• JLSteenwyk / orthosnap
  a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
  ☆26Updated 2 months ago
• PacificBiosciences / pbipa
  Improved Phased Assembler
  ☆28Updated 3 years ago