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
  ☆23Updated 4 months ago
• at-cg / RAFT
  ☆23Updated 8 months ago
• HuiyangYu / TGSFilter
  TGSFilter: An ultra-fast and efficient tool for long reads filtering and trimming
  ☆21Updated 11 months ago
• alekseyzimin / EviAnn_release
  This is the standalone version of the EviAnn pipeline
  ☆28Updated 3 weeks ago
• NBISweden / TransposonPSI
  TransposonPSI involves a PSI-blast search of a protein or nucleotide sequence against a set of profiles of proteins corresponding to majo…
  ☆13Updated 4 years ago
• davidebolo1993 / cosigt
  ☆17Updated 2 weeks ago
• simonhmartin / asynt
  Genome alignment and synteny plots
  ☆30Updated last year
• 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 last year
• PacificBiosciences / pbipa
  Improved Phased Assembler
  ☆28Updated 3 years ago
• jmsong2 / GenomeSyn
  We developed GenomeSyn as a new tool for constructing and visualizing genome synteny, its novel design and implementation can serve as a …
  ☆25Updated 3 years ago
• sanger-tol / yahs
  Yet another Hi-C scaffolding tool
  ☆19Updated 6 months ago
• dfguan / pin_hic
  A Hi-C scaffolding method
  ☆23Updated 3 years ago
• JLSteenwyk / orthosnap
  a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees
  ☆25Updated 2 months ago
• wtsi-hpag / scanPAV
  Pipeline to detect PAVs (presence/absence variations) in genome comparison using whole genome alignment.
  ☆29Updated 7 years ago
• bcgsc / ntSynt-viz
  Multi-genome synteny block visualization tool
  ☆33Updated 3 months ago
• marbl / training
  Genome Assembly 102
  ☆14Updated this week
• SandraLouise / SVJedi-graph
  SV genotyper for long reads with a variation graph
  ☆12Updated last month
• almeidasilvaf / doubletrouble
  An R package to identify and classify duplicated genes from whole-genome protein sequence data
  ☆25Updated last month
• gtrichard / mummer-ggplot
  Nucmer from Mummer3 followed by ggplot for nicer and more customisable genome alignment plots.
  ☆11Updated 4 years ago
• isugifNF / polishCLR
  A nextflow pipeline for polishing CLR assemblies
  ☆17Updated 2 years ago
• nextgenusfs / redmask
  Genome assembly soft-masking using Red (REpeat Detector)
  ☆17Updated 6 years ago
• clemgoub / rm2gff3
  Convert RepeatMasker ".out" file into a gff3 with colors!!!
  ☆21Updated 4 years ago
• Eco-Flow / synteny
  A Nextflow pipeline for running synteny analysis.
  ☆14Updated last week
• kavonrtep / dante
  Domain based annotation of transposable elements
  ☆19Updated 2 months ago
• DessimozLab / edgehog
  Infering ancestral synteny with hierarchical orthologous groups
  ☆14Updated this week
• mikolmogorov / maf2synteny
  A tool for recovering synteny blocks from multiple alignment
  ☆30Updated 3 years ago
• SamiLhll / macrosyntR
  R package for comparison of synteny conservation at the genome-wide scale.
  ☆14Updated 10 months ago
• WHops / NAHRwhals
  R package and wrapper functions for identifying serial structural variations from genome assemblies
  ☆29Updated 7 months ago
• lh3 / TRF-mod
  Tandem Repeats Finder: a program to analyze DNA sequences
  ☆14Updated 2 years ago
• GTPB / CPANG22
  Computational Pangenomics
  ☆17Updated 2 years ago