文章链接：/tseemann/prokka
的简介
快速核基因组注释
2、ProKKa的安装
在本人的使用中，有两种安装方法好用
1、用conda安装
conda install -c conda-forge -c bioconda -c defaults prokka2、用docker进行安装
docker pull staphb/prokka:latest
docker run staphb/prokka:latest prokka -hdocker需要linux系统中安装，然后使用，比conda好用
3、软件的使用
prokka --proteins --outdir mutant --prefix K12_mut
参数
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:
--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)
--locustag [X] Locus tag prefix (default 'PROKKA')
--increment [N] Locus tag counter increment (default '1')
--gffver [N] GFF version (default '3')
--compliant Force Genbank/ENA/DDJB compliance: --genes --mincontiglen 200 --centre XXX (default OFF)
--centre [X] Sequencing centre ID. (default '')
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 file of trusted proteins to first annotate from (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)
Computation:
--fast Fast mode - skip CDS /product searching (default OFF)
--cpus [N] Number of CPUs to use [0=all] (default '8')
--mincontiglen [N] Minimum contig size [NCBI needs 200] (default '1')
--evalue [] Similarity e-value cut-off (default '1e-06')
--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)
输出文件
| Extension | 描述 |
|---|---|
| .gff | This is the master annotation in GFF3 format, containing both sequences and annotations. It can be viewed directly in Artemis or IGV. |
| .gbk | This is a standard Genbank file derived from the master .gff. If the input to prokka was a multi-FASTA, then this will be a multi-Genbank, with one record for each sequence. |
| .fna | Nucleotide FASTA file of the input contig sequences. |
| .faa | Protein FASTA file of the translated CDS sequences. |
| .ffn | Nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) |
| .sqn | An ASN1 format "Sequin" file for submission to Genbank. It needs to be edited to set the correct taxonomy, authors, related publication etc. |
| .fsa | Nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file. It is mostly the same as the .fna file, but with extra Sequin tags in the sequence description lines. |
| .tbl | Feature Table file, used by "tbl2asn" to create the .sqn file. |
| .err | Unacceptable annotations - the NCBI discrepancy report. |
| .log | Contains all the output that Prokka produced during its run. This is a record of what settings you used, even if the --quiet option was enabled. |
| .txt | Statistics relating to the annotated features found. |
| .tsv | Tab-separated file of all features: locus_tag,ftype,len_bp,gene,EC_number,COG,product |
当用prokka进行批量注释时
for i in *.fna; do k=`echo $i | sed 's/.fna//g'` && prokka $i --prefix $k -outdir $k --cpus 24; done注：使用使应注意自己的fasta文件格式，尾缀是.fna .fa .fasta等,前后都要改
注释完成后，提取结果文件
mkdir outlet
cp */*.gff outlet注：提取不同格式的文件，记得更改文件的后缀