{"id":27303116,"url":"https://github.com/tseemann/barrnap","last_synced_at":"2025-04-12T02:50:08.478Z","repository":{"id":9862800,"uuid":"11860359","full_name":"tseemann/barrnap","owner":"tseemann","description":":microscope: :leo: Bacterial ribosomal RNA 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Status](https://travis-ci.org/tseemann/barrnap.svg?branch=master)](https://travis-ci.org/tseemann/barrnap) [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) [](#lang-au)\n\n# Barrnap\n\nBAsic Rapid Ribosomal RNA Predictor\n\n## Description\n\nBarrnap predicts the location of ribosomal RNA genes in genomes.\nIt supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S),\nmetazoan mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S).\n\nIt takes FASTA DNA sequence as input, and write GFF3 as output.\nIt uses the new `nhmmer` tool that comes with HMMER 3.1 for HMM searching in RNA:DNA style.\nMultithreading is supported and one can expect roughly linear speed-ups with more CPUs.\n\n## Installation\n\n### Requirements\n* [Perl 5.xx](https://dev.perl.org/perl5/) (core modules only)\n* [nhmmer](https://hmmer.org/) (part of HMMER 3.x)\n* [bedtools \u003e= 2.27.0](http://bedtools.readthedocs.io/en/latest/)\n\n### Conda\nInstall [Conda](https://conda.io/docs/) or [Miniconda](https://conda.io/miniconda.html):\n```\nconda install -c bioconda -c conda-forge barrnap\n```\n\n### Homebrew\nInstall [Homebrew](http://brew.sh/) (macOS) or [Linuxbrew](http://brew.sh/linuxbrew/) (Linux).\n```\nbrew install brewsci/bio/barrnap\n```\n\n### Source\nThis will install the latest version direct from Github. \nYou'll need to add the `bin` directory to your `PATH`.\n```\ncd $HOME\ngit clone https://github.com/tseemann/barrnap.git\ncd barrnap/bin\n./barrnap --help\n```\n\n## Usage\n\n```\n% barrnap --quiet examples/small.fna\n##gff-version 3\nP.marinus\tbarrnap:0.8\trRNA\t353314\t354793\t0\t+\t.\tName=16S_rRNA;product=16S ribosomal RNA\nP.marinus\tbarrnap:0.8\trRNA\t355464\t358334\t0\t+\t.\tName=23S_rRNA;product=23S ribosomal RNA\nP.marinus\tbarrnap:0.8\trRNA\t358433\t358536\t7.5e-07\t+\t.\tName=5S_rRNA;product=5S ribosomal RNA\n\n% barrnap -q -k mito examples/mitochondria.fna \n##gff-version 3\nAF346967.1\tbarrnap:0.8\trRNA\t643\t1610\t.\t+\t.\tName=12S_rRNA;product=12S ribosomal RNA\nAF346967.1\tbarrnap:0.8\trRNA\t1672\t3228\t.\t+\t.\tName=16S_rRNA;product=16S ribosomal RNA\n  \n% barrnap -o rrna.fa \u003c contigs.fa \u003e rrna.gff\n% head -n 3 rrna.fa\n\u003e16S_rRNA::gi|329138943|tpg|BK006945.2|:455935-456864(-)\nACGGTCGGGGGCATCAGTATTCAATTGTCAGAGGTGAAATTCTTGGATT\nTATTGAAGACTAACTACTGCGAAAGCATTTGCCAAGGACGTTTTCATTA\n```\n\n## Options\n\n### General\n* `--help` show help and exit\n* `--version` print version in form `barrnap X.Y` and exit \n* `--citation` print a citation and exit\n### Search\n* `--kingdom` is the database to use: Bacteria:`bac`, Archaea:`arc`, Eukaryota:`euk`, Metazoan Mitochondria:`mito`\n* `--threads` is how many CPUs to assign to `nhmmer` search\n* `--evalue` is the cut-off for `nhmmer` reporting, before further scrutiny\n* `--lencutoff` is the proportion of the full length that qualifies as `partial` match\n* `--reject` will not include hits below this proportion of the expected length\n### Output\n* `--quiet` will not print any messages to `stderr`\n* `--incseq` will include the full input sequences in the output GFF\n* `--outseq` creates a FASTA file with the hit sequences\n\n## Caveats\n\nBarrnap does not do anything fancy. It has HMM models for each different rRNA gene. \nThey are built from full length seed alignments. \n\n## Comparison with RNAmmer\n\nBarrnap is designed to be a substitute for [RNAmmer](http://www.cbs.dtu.dk/services/RNAmmer/). \nIt was motivated by my desire to remove [Prokka's](https://github.com/tseemann/prokka)\ndependency on RNAmmer which is encumbered by a free-for-academic sign-up\nlicense, and by RNAmmer's dependence on legacy HMMER 2.x which conflicts\nwith HMMER 3.x that most people are using now.\n\nRNAmmer is more sophisticated than Barrnap, and more accurate because it\nuses HMMER 2.x in glocal alignment mode whereas NHMMER 3.x currently only\nsupports local alignment (Sean Eddy expected glocal to be supported in 2014, \nbut it still isn't available in 2018). \n\nIn practice, Barrnap will find all the typical rRNA genes in a few seconds\n(in bacteria), but may get the end points out by a few bases and will\nprobably miss wierd rRNAs.  The HMM models it uses are derived from Rfam,\nSilva and RefSeq.\n\n## Data sources for HMM models\n\n```\nBacteria (70S)  \n        LSU 50S\n                5S      RF00001\n                23S     SILVA-LSU-Bac\n        SSU 30S\n                16S     RF00177\n\nArchaea (70S)   \n        LSU 50S\n                5S      RF00001\n                5.8S    RF00002\n                23S     SILVA-LSU-Arc\n        SSU 30S\n                16S     RF01959\n\nEukarya (80S)   \n        LSU 60S\n                5S      RF00001\n                5.8S    RF00002\n                28S     SILVA-LSU-Euk\n        SSU 40S\n                18S     RF01960\n\nMetazoan Mito\n                12S     RefSeq (MT-RNR1, s-rRNA, rns)\n                16S     RefSeq (MT-RNR2, l-rRNA, rnl)       \n```\n\n## Models I would like to add\n\n```\nFungi\t[Sajeet Haridas]\n        LSU 35S ?\n                5S\n                5.8S\n                25S\n        SSU ?\n                18S\n        Mito [http://www.ncbi.nlm.nih.gov/nuccore/NC_001224.1]\n                15S \n                21S (multiple exons)\n                \nApicoplast [http://www.ncbi.nlm.nih.gov/nuccore/U87145.2]\n                LSU ~2500bp 28S ?\n                SSU ~1500bp 16S ?\n\nPlant [Shaun Jackman]\n\tMito [https://www.ncbi.nlm.nih.gov/nucleotide?cmd=Retrieve\u0026dopt=GenBank\u0026list_uids=26556996]\t\n\t\t5S\t~118 bp  ?\trrn5 \t(use RF00001 ?)\n\t\t18S\t~1935 bp ?\trrn18\t(use RF01960 ?)\n\t\t26S\t~2568 bp ?\trrn26   \n```\n\n## Where does the name come from?\n\nThe name Barrnap was originally derived from _Bacterial/Archaeal Ribosomal RNA Predictor_.\nHowever it has since been extended to support mitochondrial and eukaryotic rRNAs, and has been\ngiven the new backronym _BAsic Rapid Ribosomal RNA Predictor_.\nThe project was originally spawned at CodeFest 2013 in Berlin, Germany \nby Torsten Seemann and Tim Booth.\n\n## License\n\n* Barrnap: [GPLv3](https://raw.githubusercontent.com/tseemann/barrnap/master/LICENSE)\n* Rfam: [CC0](https://raw.githubusercontent.com/tseemann/barrnap/master/LICENSE.Rfam)\n* SILVA: [Free for academic use](https://raw.githubusercontent.com/tseemann/barrnap/master/LICENSE.SILVA)\n\n## Author\n\nTorsten Seemann\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftseemann%2Fbarrnap","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ftseemann%2Fbarrnap","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ftseemann%2Fbarrnap/lists"}