Alternatives and similar repositories for medaka:

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

• rrwick / Porechop
  adapter trimmer for Oxford Nanopore reads
  ☆356Updated 11 months ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆357Updated 3 years ago
• wdecoster / NanoPlot
  Plotting scripts for long read sequencing data
  ☆468Updated 2 months ago
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆326Updated last year
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆345Updated last month
• 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…
  ☆278Updated 11 months ago
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆500Updated 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…
  ☆397Updated 2 months ago
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆318Updated 10 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆226Updated 4 years ago
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆820Updated 7 months ago
• chhylp123 / hifiasm
  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
  ☆596Updated 3 weeks ago
• ablab / quast
  Genome assembly evaluation tool
  ☆427Updated 5 months ago
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆332Updated this week
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆497Updated last month
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆584Updated 3 weeks ago
• Nextomics / NextDenovo
  Fast and accurate de novo assembler for long reads
  ☆388Updated 11 months ago
• rrwick / Unicycler
  hybrid assembly pipeline for bacterial genomes
  ☆592Updated 8 months ago
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆367Updated 7 months ago
• 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
• mummer4 / mummer
  Mummer alignment tool
  ☆495Updated 2 months ago
• pangenome / pggb
  the pangenome graph builder
  ☆423Updated this week
• agshumate / Liftoff
  An accurate GFF3/GTF lift over pipeline
  ☆476Updated last year
• schneebergerlab / syri
  Synteny and Rearrangement Identifier
  ☆374Updated 2 weeks ago
• PacificBiosciences / pbbioconda
  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
  ☆266Updated 2 months ago
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆333Updated last year
• TransDecoder / TransDecoder
  TransDecoder source
  ☆288Updated 6 months ago
• usadellab / Trimmomatic
  ☆242Updated 10 months ago
• wyp1125 / MCScanX
  MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
  ☆253Updated 3 months ago
• wdecoster / nanopack
  An overview of all nanopack tools
  ☆239Updated last year