Alternatives and similar repositories for bonito

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

• nanoporetech / medaka
  Sequence correction provided by ONT Research
  ☆482Updated last month
• wdecoster / NanoPlot
  Plotting scripts for long read sequencing data
  ☆504Updated last month
• chhylp123 / hifiasm
  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
  ☆680Updated 6 months ago
• mummer4 / mummer
  Mummer alignment tool
  ☆526Updated 8 months ago
• nanoporetech / dorado
  Oxford Nanopore's Basecaller
  ☆735Updated last month
• kishwarshafin / pepper
  PEPPER-Margin-DeepVariant
  ☆252Updated last year
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆620Updated last month
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆534Updated last year
• rrwick / Porechop
  adapter trimmer for Oxford Nanopore reads
  ☆373Updated last year
• ComparativeGenomicsToolkit / cactus
  Official home of genome aligner based upon notion of Cactus graphs
  ☆615Updated this week
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆554Updated this week
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆874Updated 5 months ago
• pangenome / pggb
  the pangenome graph builder
  ☆455Updated 2 months ago
• ablab / quast
  Genome assembly evaluation tool
  ☆467Updated 10 months ago
• gamcil / clinker
  Gene cluster comparison figure generator
  ☆615Updated 10 months ago
• bcgsc / NanoSim
  Nanopore sequence read simulator
  ☆284Updated 7 months ago
• rrwick / Unicycler
  hybrid assembly pipeline for bacterial genomes
  ☆618Updated 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…
  ☆426Updated 8 months ago
• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆365Updated 3 months ago
• GoekeLab / awesome-nanopore
  A curated list of awesome nanopore analysis tools.
  ☆296Updated 3 months ago
• moshi4 / pyGenomeViz
  A genome visualization python package for comparative genomics
  ☆368Updated last week
• nanoporetech / ont_fast5_api
  Oxford Nanopore Technologies fast5 API software
  ☆154Updated last year
• lh3 / miniprot
  Align proteins to genomes with splicing and frameshift
  ☆380Updated 3 weeks 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…
  ☆287Updated last year
• HKU-BAL / Clair3
  Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling
  ☆304Updated 2 weeks ago
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆355Updated last week
• agshumate / Liftoff
  An accurate GFF3/GTF lift over pipeline
  ☆507Updated 2 years ago
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆439Updated 9 months ago
• bioconvert / bioconvert
  Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
  ☆383Updated 3 months ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆513Updated last month