Alternatives and similar repositories for funannotate:

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

• 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…
  ☆390Updated last month
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆323Updated last year
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆316Updated 9 months ago
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆353Updated 2 years ago
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆300Updated last month
• rrwick / Porechop
  adapter trimmer for Oxford Nanopore reads
  ☆353Updated 10 months ago
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆495Updated last year
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆221Updated 4 years ago
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆488Updated last week
• tseemann / mlst
  Scan contig files against PubMLST typing schemes
  ☆218Updated 2 years ago
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆329Updated last year
• gtonkinhill / panaroo
  An updated pipeline for pangenome investigation
  ☆288Updated 2 weeks ago
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆238Updated last year
• TransDecoder / TransDecoder
  TransDecoder source
  ☆285Updated 5 months ago
• ndierckx / NOVOPlasty
  NOVOPlasty - The organelle assembler and heteroplasmy caller
  ☆184Updated last year
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆330Updated last week
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆362Updated 6 months ago
• schneebergerlab / syri
  Synteny and Rearrangement Identifier
  ☆367Updated 3 weeks ago
• nanoporetech / medaka
  Sequence correction provided by ONT Research
  ☆442Updated 5 months ago
• jiarong / VirSorter2
  customizable pipeline to identify viral sequences from (meta)genomic data
  ☆240Updated 3 months ago
• jtlovell / GENESPACE
  ☆199Updated last month
• MrOlm / drep
  Rapid comparison and dereplication of genomes
  ☆277Updated 3 months ago
• NBISweden / GAAS
  Genome Assembly and Annotation Service code
  ☆209Updated last year
• agshumate / Liftoff
  An accurate GFF3/GTF lift over pipeline
  ☆471Updated last year
• sortmerna / sortmerna
  SortMeRNA: next-generation sequence filtering and alignment tool
  ☆255Updated 2 months ago
• Gaius-Augustus / Augustus
  Genome annotation with AUGUSTUS
  ☆296Updated 2 months ago
• Dfam-consortium / RepeatMasker
  RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  ☆247Updated last week
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆337Updated 2 years ago
• wyp1125 / MCScanX
  MCScanX: Multiple Collinearity Scan toolkit X version. The most popular synteny analysis tool in the world!
  ☆251Updated 3 months ago
• Nextomics / NextDenovo
  Fast and accurate de novo assembler for long reads
  ☆381Updated 10 months ago