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…
  ☆419Updated 6 months ago
• ncbi / pgap
  NCBI Prokaryotic Genome Annotation Pipeline
  ☆345Updated 2 weeks ago
• rrwick / Porechop
  adapter trimmer for Oxford Nanopore reads
  ☆367Updated last year
• Ecogenomics / CheckM
  Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  ☆377Updated last month
• schneebergerlab / plotsr
  Tool to plot synteny and structural rearrangements between genomes
  ☆317Updated 4 months ago
• jenniferlu717 / KrakenTools
  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
  ☆347Updated last week
• rrwick / Trycycler
  A tool for generating consensus long-read assemblies for bacterial genomes
  ☆327Updated last year
• broadinstitute / pilon
  Pilon is an automated genome assembly improvement and variant detection tool
  ☆367Updated 3 years ago
• BioInfoTools / BBMap
  (Not Offical) BBMap short read aligner, and other bioinformatic tools.
  ☆236Updated 4 years ago
• Gaius-Augustus / Augustus
  Genome annotation with AUGUSTUS
  ☆313Updated last month
• schneebergerlab / syri
  Synteny and Rearrangement Identifier
  ☆403Updated 3 months ago
• tseemann / barrnap
  Bacterial ribosomal RNA predictor
  ☆249Updated last year
• rrwick / Filtlong
  quality filtering tool for long reads
  ☆358Updated last year
• malonge / RagTag
  Tools for fast and flexible genome assembly scaffolding and improvement
  ☆520Updated last year
• MrOlm / drep
  Rapid comparison and dereplication of genomes
  ☆304Updated last month
• nanoporetech / medaka
  Sequence correction provided by ONT Research
  ☆468Updated 2 months ago
• biobakery / MetaPhlAn
  MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
  ☆355Updated last month
• tseemann / mlst
  Scan contig files against PubMLST typing schemes
  ☆239Updated 2 years ago
• sanger-pathogens / Roary
  Rapid large-scale prokaryote pan genome analysis
  ☆354Updated 3 years ago
• mummer4 / mummer
  Mummer alignment tool
  ☆521Updated 6 months ago
• bxlab / metaWRAP
  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
  ☆434Updated 2 years ago
• ablab / quast
  Genome assembly evaluation tool
  ☆451Updated 8 months ago
• marbl / verkko
  Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and O…
  ☆354Updated last month
• ParBLiSS / FastANI
  Fast Whole-Genome Similarity (ANI) Estimation
  ☆422Updated 2 weeks ago
• arpcard / rgi
  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on h…
  ☆379Updated last week
• labgem / PPanGGOLiN
  Build a partitioned pangenome graph from microbial genomes
  ☆275Updated last month
• Nextomics / NextDenovo
  Fast and accurate de novo assembler for long reads
  ☆390Updated last year
• shenwei356 / taxonkit
  A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
  ☆430Updated 3 months ago
• usadellab / Trimmomatic
  ☆259Updated last week
• oschwengers / bakta
  Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
  ☆540Updated last month