Alternatives and similar repositories for minigraph:

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

• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆584Updated this week
• pangenome / pggb
  the pangenome graph builder
  ☆420Updated last month
• fritzsedlazeck / SURVIVOR
  Toolset for SV simulation, comparison and filtering
  ☆376Updated last year
• chhylp123 / hifiasm
  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
  ☆591Updated last week
• maickrau / GraphAligner
  ☆268Updated 3 months ago
• Nextomics / NextDenovo
  Fast and accurate de novo assembler for long reads
  ☆384Updated 10 months ago
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆499Updated last year
• philres / ngmlr
  NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on r…
  ☆297Updated last year
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆246Updated 2 weeks ago
• ComparativeGenomicsToolkit / cactus
  Official home of genome aligner based upon notion of Cactus graphs
  ☆561Updated this week
• lh3 / miniasm
  Ultrafast de novo assembly for long noisy reads (though having no consensus step)
  ☆320Updated last year
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆267Updated last month
• HKU-BAL / Clair3
  Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
  ☆270Updated last week
• ACEnglish / truvari
  Structural variant toolkit for VCFs
  ☆348Updated 3 weeks ago
• schneebergerlab / syri
  Synteny and Rearrangement Identifier
  ☆371Updated last month
• marbl / Winnowmap
  Long read / genome alignment software
  ☆281Updated 4 months ago
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆257Updated 2 months ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆354Updated 2 years ago
• Gaius-Augustus / BRAKER
  BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eu…
  ☆392Updated 2 months ago
• isovic / racon
  Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr…
  ☆279Updated 10 months ago
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆324Updated last year
• agshumate / Liftoff
  An accurate GFF3/GTF lift over pipeline
  ☆474Updated last year
• lastz / lastz
  Program for aligning DNA sequences, a pairwise aligner.
  ☆216Updated this week
• nf-core / nanoseq
  Nanopore demultiplexing, QC and alignment pipeline
  ☆194Updated this week
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆276Updated 5 months ago
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆317Updated 10 months ago
• mummer4 / mummer
  Mummer alignment tool
  ☆491Updated last month
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆239Updated 11 months ago
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆425Updated this week
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆237Updated last year