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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/bakta commit bf30715c881a622947d3d099d7a22e323e2ceef3-dirty"
author pimarin
date Wed, 18 May 2022 11:13:45 +0000
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children 728e602cd3f7
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-1:000000000000 0:4d315de96666
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@TOOL_VERSION@">1.4.0</token>
4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@PROFILE@">22.01</token>
6 <xml name="version_command">
7 <version_command><![CDATA[rcf -V]]></version_command>
8 </xml>
9 <xml name="xrefs">
10 <xrefs>
11 <xref type='bio.tools'>Bakta</xref>
12 </xrefs>
13 </xml>
14 <xml name="requirements">
15 <requirements>
16 <requirement type="package" version="@TOOL_VERSION@">bakta</requirement>
17 </requirements>
18 </xml>
19 <xml name="citations">
20 <citations>
21 <citation type="bibtex">
22 @article{mbs:/content/journal/mgen/10.1099/mgen.0.000685,
23 author = "Schwengers, Oliver and Jelonek, Lukas and Dieckmann, Marius Alfred and Beyvers, Sebastian and Blom, Jochen and Goesmann, Alexander",
24 title = "Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification",
25 journal= "Microbial Genomics",
26 year = "2021",
27 volume = "7",
28 number = "11",
29 pages = "",
30 doi = "https://doi.org/10.1099/mgen.0.000685",
31 url = "https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000685",
32 publisher = "Microbiology Society",
33 issn = "2057-5858",
34 type = "Journal Article",
35 keywords = "whole-genome sequencing",
36 keywords = "bacteria",
37 keywords = "metagenome-assembled genomes",
38 keywords = "plasmids ",
39 keywords = "genome annotation",
40 eid = "000685",
41 abstract = "Command-line annotation software tools have continuously gained popularity compared to
42 centralized online services due to the worldwide increase of sequenced bacterial genomes.
43 However, results of existing command-line software pipelines heavily depend on taxon-specific
44 databases or sufficiently well annotated reference genomes. Here, we introduce Bakta, a new command-line
45 software tool for the robust, taxon-independent, thorough and, nonetheless, fast annotation of bacterial genomes.
46 Bakta conducts a comprehensive annotation workflow including the detection of small proteins taking into account
47 replicon metadata. The annotation of coding sequences is accelerated via an alignment-free sequence identification
48 approach that in addition facilitates the precise assignment of public database cross-references.
49 Annotation results are exported in GFF3 and International Nucleotide Sequence Database Collaboration (INSDC)-compliant flat files,
50 as well as comprehensive JSON files, facilitating automated downstream analysis.
51 We compared Bakta to other rapid contemporary command-line annotation software tools in both targeted and taxonomically broad benchmarks
52 including isolates and metagenomic-assembled genomes. We demonstrated that Bakta outperforms other tools in terms of functional annotations,
53 the assignment of functional categories and database cross-references, whilst providing comparable wall-clock runtimes.
54 Bakta is implemented in Python 3 and runs on MacOS and Linux systems.
55 It is freely available under a GPLv3 license at https://github.com/oschwengers/bakta.
56 An accompanying web version is available at https://bakta.computational.bio.",
57 }
58 </citation>
59 </citations>
60 </xml>
61 </macros>