Prokka 的使用

Prokka可以对原核基因组和宏基因组进行快速的功能注释。

参考资料：

http://blog.sciencenet.cn/blog-3334560-1199422.html

https://mp.weixin.qq.com/s/1TM61IrzrpVb5KhZ5A0kZQ?

http://www.chinapubmed.net/24642063

安装

#依赖于conda，所以支持conda安装
conda install Prokka
# 自动搜索并添加数据库
prokka --setupdb
# 测序数据库
prokka --listdb

运行Prokka注释contig

#usage
Usage:
 prokka [options] <contigs.fasta>
General:
 --help             This help
 --version          Print version and exit
 --citation         Print citation for referencing Prokka
 --quiet            No screen output (default OFF)
 --debug            Debug mode: keep all temporary files (default OFF)
Setup:
 --dbdir [X]        Prokka database root folders (default '/home6/trainees/miniconda3/db')
 --listdb           List all configured databases
 --setupdb          Index all installed databases
 --cleandb          Remove all database indices
 --depends          List all software dependencies
Outputs:
 --outdir [X]       Output folder [auto] (default '')
 --force            Force overwriting existing output folder (default OFF)
 --prefix [X]       Filename output prefix [auto] (default '')
 --addgenes         Add 'gene' features for each 'CDS' feature (default OFF)
 --addmrna          Add 'mRNA' features for each 'CDS' feature (default OFF)
 --locustag [X]     Locus tag prefix [auto] (default '')
 --increment [N]    Locus tag counter increment (default '1')
 --gffver [N]       GFF version (default '3')
 --compliant        Force Genbank/ENA/DDJB compliance: --addgenes --mincontiglen 200 --centre XXX (default OFF)
 --centre [X]       Sequencing centre ID. (default '')
 --accver [N]       Version to put in Genbank file (default '1')
Organism details:
 --genus [X]        Genus name (default 'Genus')
 --species [X]      Species name (default 'species')
 --strain [X]       Strain name (default 'strain')
 --plasmid [X]      Plasmid name or identifier (default '')
Annotations:
 --kingdom [X]      Annotation mode: Archaea|Bacteria|Mitochondria|Viruses (default 'Bacteria')
 --gcode [N]        Genetic code / Translation table (set if --kingdom is set) (default '0')
 --prodigaltf [X]   Prodigal training file (default '')
 --gram [X]         Gram: -/neg +/pos (default '')
 --usegenus         Use genus-specific BLAST databases (needs --genus) (default OFF)
 --proteins [X]     FASTA or GBK file to use as 1st priority (default '')
 --hmms [X]         Trusted HMM to first annotate from (default '')
 --metagenome       Improve gene predictions for highly fragmented genomes (default OFF)
 --rawproduct       Do not clean up /product annotation (default OFF)
 --cdsrnaolap       Allow [tr]RNA to overlap CDS (default OFF)
Matching:
 --evalue [n.n]     Similarity e-value cut-off (default '1e-09')
 --coverage [n.n]   Minimum coverage on query protein (default '80')
Computation:
 --cpus [N]         Number of CPUs to use [0=all] (default '8')
 --fast             Fast mode - only use basic BLASTP databases (default OFF)
 --noanno           For CDS just set /product="unannotated protein" (default OFF)
 --mincontiglen [N] Minimum contig size [NCBI needs 200] (default '1')
 --rfam             Enable searching for ncRNAs with Infernal+Rfam (SLOW!) (default '0')
 --norrna           Don't run rRNA search (default OFF)
 --notrna           Don't run tRNA search (default OFF)
 --rnammer          Prefer RNAmmer over Barrnap for rRNA prediction (default OFF)</pre>

Example

prokka final.contigs.fa --outdir prokka_annotation --prefix metagG --metagenome --kingdom Bacteria
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我目前的需求超级简单，就是对一个细菌基因组进行快速注释，如果我有更高需求的话，再来更新。