Alternatives and similar repositories for pilon:

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

• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆314Updated 8 months ago
• a-slide / pycoQC
  pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies b…
  ☆273Updated 3 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆215Updated 3 years ago
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆310Updated last year
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆230Updated last year
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆330Updated last week
• 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…
  ☆276Updated 8 months ago
• wdecoster / nanofilt
  Filtering and trimming of long read sequencing data
  ☆197Updated 2 years ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆240Updated 2 months ago
• jenniferlu717 / Bracken
  Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species i…
  ☆299Updated 6 months ago
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆486Updated 11 months ago
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆326Updated last year
• 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…
  ☆374Updated last week
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆259Updated 7 months ago
• sanger-pathogens / circlator
  A tool to circularize genome assemblies
  ☆235Updated 9 months ago
• wyp1125 / MCScanX
  MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
  ☆247Updated last month
• 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…
  ☆295Updated 10 months ago
• rrwick / Porechop
  adapter trimmer for Oxford Nanopore reads
  ☆348Updated 8 months ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆294Updated 2 months ago
• marbl / verkko
  Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…
  ☆315Updated this week
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆206Updated last year
• TransDecoder / TransDecoder
  TransDecoder source
  ☆283Updated 3 months ago
• nanoporetech / medaka
  Sequence correction provided by ONT Research
  ☆435Updated 3 months ago
• Nextomics / NextPolish
  Fast and accurately polish the genome generated by long reads.
  ☆217Updated 3 weeks ago
• Nextomics / NextDenovo
  Fast and accurate de novo assembler for long reads
  ☆376Updated 8 months ago
• schneebergerlab / syri
  Synteny and Rearrangement Identifier
  ☆357Updated last month
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆232Updated last year
• tseemann / mlst
  Scan contig files against PubMLST typing schemes
  ☆210Updated 2 years ago
• PacificBiosciences / IsoSeq
  Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
  ☆200Updated 3 months ago
• aidenlab / 3d-dna
  3D de novo assembly (3D DNA) pipeline
  ☆207Updated last year