Alternatives and similar repositories for BRAKER

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

• nextgenusfs / funannotate
  Eukaryotic Genome Annotation Pipeline
  ☆356Updated last week
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆516Updated last year
• schneebergerlab / syri
  Synteny and Rearrangement Identifier
  ☆396Updated 2 months ago
• rrwick / Porechop
  adapter trimmer for Oxford Nanopore reads
  ☆365Updated last year
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆367Updated 3 years ago
• pangenome / pggb
  the pangenome graph builder
  ☆439Updated last month
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆376Updated last month
• oushujun / EDTA
  Extensive de-novo TE Annotator
  ☆392Updated 2 weeks ago
• TransDecoder / TransDecoder
  TransDecoder source
  ☆292Updated 9 months ago
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆345Updated last year
• Nextomics / NextDenovo
  Fast and accurate de novo assembler for long reads
  ☆388Updated last year
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆342Updated last month
• mummer4 / mummer
  Mummer alignment tool
  ☆518Updated 5 months ago
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆354Updated 3 years ago
• agshumate / Liftoff
  An accurate GFF3/GTF lift over pipeline
  ☆490Updated last year
• ablab / quast
  Genome assembly evaluation tool
  ☆445Updated 8 months ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆235Updated 4 years ago
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆532Updated last week
• nanoporetech / medaka
  Sequence correction provided by ONT Research
  ☆465Updated last month
• marbl / verkko
  Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…
  ☆352Updated 2 weeks ago
• wyp1125 / MCScanX
  MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
  ☆259Updated 6 months ago
• usadellab / Trimmomatic
  ☆256Updated last year
• rrwick / Unicycler
  hybrid assembly pipeline for bacterial genomes
  ☆602Updated 11 months ago
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆351Updated last year
• Gaius-Augustus / Augustus
  Genome annotation with AUGUSTUS
  ☆310Updated last week
• wdecoster / NanoPlot
  Plotting scripts for long read sequencing data
  ☆486Updated 2 months ago
• tseemann / abricate
  Mass screening of contigs for antimicrobial and virulence genes
  ☆428Updated last year
• ComparativeGenomicsToolkit / cactus
  Official home of genome aligner based upon notion of Cactus graphs
  ☆589Updated this week
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆311Updated 3 months ago
• chhylp123 / hifiasm
  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
  ☆654Updated 3 months ago