prokka-原核及病毒基因组高效便捷注释

简介

Prokka: rapid prokaryotic genome annotation
全基因组注释是在一组基因组DNA序列中识别感兴趣的特征，并用有用的信息标记它们的过程。Prokka是一款软件工具，可以快速注释细菌、古菌和病毒基因组，并生成符合标准的输出文件。

安装

conda create prokka -c conda-forge -c bioconda -c defaults prokka=1.14
# 1.13版本会报blastp <2.2，实际上已经安装blastp 2.10

• Test
  Type prokka and it should output its help screen.
  Type prokka --version and you should see an output like prokka 1.x
  Type prokka --listdb and it will show you what databases it has installed to use.

• 运行时出现如下报错则重新按照上述命令安装。

[20:43:45] Prokka needs blastp 2.2 or higher. Please upgrade and try again.

使用

 prokka contigs.fa
# Look for a folder called PROKKA_yyyymmdd (today's date) and look at stats
prokka --force --outdir mydir --prefix mygenome contigs.fa

time prokka  --force --cpu 100 --outdir ecoli_prokka --prefix ecoli  ../Ecoli_k12/Ecoli_k12.fasta
#  大肠杆菌8核1min30s，100核50s

• 预测病毒基因

nohup time prokka --force  --centre X --compliant --cpus 80 --kingdom  Viruses --outdir Viruses_kingdom  --prefix 
../Viral_prediction/Virsorter_Virfinder_Deepvirfinder_share_at_least_two_method.fa &>prokka.log&

nohup time prokka  --cpus 80 --kingdom  Viruses --outdir Viruses_kingdom  ../Viral_prediction/Virsorter_Virfinder_Deepvirfinder_share_at_least_two_method.fa &>prokka.log&

Contig ID must <= 37 chars long: k141_4519235_length_122628_cov_55.0330

• 默认使用Barrnap 预测rRNA

–rnammer Prefer RNAmmer over Barrnap for rRNA prediction (default OFF)

耗时

原核生物基因组在1-10min之内完成，平均在3min；
10015个基因组同时并行20个任务，平均耗时1.77m，总耗时1141m51.958s.

结果

PROKKA_11092023.txt

organism: Genus species strain
contigs: 628
bases: 4038506
CDS: 3936
gene: 3979
rRNA: 1
tRNA: 41
tmRNA: 1

PROKKA_11092023.faa：蛋白序列

>CBEGICMN_00001 hypothetical protein
MKTIASWLFALGGLFMGSPACAGAIDAGRLATVDAHALAATVQSEVTILSLAQYLGAGAS
SDVEKARAVYRWVADRIAYDAKSFFNQTHPSVDPNAVFQSRLAACGGYAALFERVAKESG
LEATTIIGYAKGIAHIAGGSMAEPNHAWNAVKIDGKWQLIDTTWGSGYVSDGAYVKQFSE
TFFLPSPEQLAFSHFPQDAAWQLRSERSLSKTEFESLPEINTAFFNLGIDPSDVWKTVKS
QEFKGALVHTFDLPAGVAKVRNAPLSYQLPVGSTQHFEIVSASFEKMAVEYNKKWLPMQK
KGDVFSIEIAAKSKGELSVNGKTPTSRKHATVLEYIVD
>CBEGICMN_00002 hypothetical protein
MSPVPSNAADSPLDETPESLTPQEFDEIDAILDDLRTRYDETPHWEFCEGFMAALICCRR
LIMPSEYLPELLALGVNGEVDEGSFADDAQFNRFMALWARRWNEVAHALNAKIENLGDEA

PROKKA_11092023.ffn：基因核酸序列，与蛋白序列ID一致

>CBEGICMN_00001 hypothetical protein
ATGAAGACGATCGCTTCCTGGCTCTTTGCCTTGGGCGGATTGTTCATGGGTAGCCCTGCT
TGCGCTGGCGCTATTGATGCTGGCCGCCTTGCCACCGTTGATGCCCACGCCTTGGCCGCG
ACCGTTCAATCTGAAGTGACGATTCTGTCCCTTGCGCAGTATCTCGGCGCGGGGGCTAGT
AGCGATGTTGAAAAAGCCCGCGCGGTATATCGTTGGGTCGCGGATCGCATTGCCTACGAT
GCCAAGAGCTTTTTTAACCAAACACACCCAAGCGTTGATCCTAATGCCGTATTCCAATCG
CGCCTTGCAGCCTGCGGCGGTTACGCTGCATTGTTCGAGCGCGTTGCCAAGGAGTCCGGG
TTGGAGGCTACCACCATTATTGGCTATGCGAAAGGCATTGCCCACATAGCCGGAGGTAGC
ATGGCCGAGCCGAATCATGCTTGGAATGCTGTAAAAATTGACGGCAAGTGGCAGCTCATT
GACACGACCTGGGGCAGTGGTTACGTAAGCGATGGTGCCTATGTAAAGCAGTTCAGCGAA

PROKKA_11092023.fna：拷贝基因组文件

>gnl|X|CBEGICMN_1
CCGCCAGCCTGAGCCCTATTGATGTGCACTTCGCTATTGCAATCCGACAGAAAAGTTATG
GCGCCATTTTCCGATCAGAACAAAGCACGAAAAGAAGAGAATGACTTGTTAGCCGGCAAC

PROKKA_11092023.fsa：

>gnl|X|CBEGICMN_1 [gcode=11] [organism=Genus species] [strain=strain]
CCGCCAGCCTGAGCCCTATTGATGTGCACTTCGCTATTGCAATCCGACAGAAAAGTTATG
GCGCCATTTTCCGATCAGAACAAAGCACGAAAAGAAGAGAATGACTTGTTAGCCGGCAAC

PROKKA_11092023.gbk：gbk文件

LOCUS       CBEGICMN_1            140756 bp    DNA     linear       09-11月-2023
DEFINITION