Team I Functional Annotation Group: Difference between revisions
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Command: | Command: | ||
<pre>prokka --outdir <output_directory> --kingdom <species' kingdom> --genus <species' genus> --gram <> --prefix <output_file> --rfam --rnammer <input_file> </pre> | <pre>prokka --outdir <output_directory> --kingdom <species' kingdom> --genus <species' genus> --gram <> --prefix <output_file> --rfam --rnammer <input_file> </pre> | ||
Runtime: ~ 16mins /genome | * Runtime: ~ 16mins /genome | ||
'''Eggnog''' | '''Eggnog''' | ||
| Line 23: | Line 23: | ||
Command: | Command: | ||
<pre>pilercr -in <input_file> -out <output_file></pre> | <pre>pilercr -in <input_file> -out <output_file></pre> | ||
Runtime: <5 sec/genome | * Runtime: <5 sec/genome | ||
'''Phobius''' | '''Phobius''' | ||
| Line 29: | Line 29: | ||
Command: | Command: | ||
<pre>phobius.pl -<output_format> <input_file> > <output_file></pre> | <pre>phobius.pl -<output_format> <input_file> > <output_file></pre> | ||
Runtime: 12-16mins /genome | * Runtime: 12-16mins /genome | ||
'''LipoP''' | '''LipoP''' | ||
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Command: | Command: | ||
<pre>tmhmm -<output_format> -<input_file> <output_file></pre> | <pre>tmhmm -<output_format> -<input_file> <output_file></pre> | ||
Runtime: ~6mins /genome | * Runtime: ~6mins /genome | ||
'''SignalP''' | '''SignalP''' | ||
| Line 47: | Line 47: | ||
Command: | Command: | ||
<pre>signalp -t <organism_type> -f <output_format> <input_file></pre> | <pre>signalp -t <organism_type> -f <output_format> <input_file></pre> | ||
Runtime: ~ 4mins /genome | * Runtime: ~ 4mins /genome | ||
'''DeepARG''' | '''DeepARG''' | ||
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Command: | Command: | ||
<pre></pre> | <pre></pre> | ||
* Runtime: 3min27s /genome | |||
'''Interproscan''' | '''Interproscan''' | ||
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* -iprlookup: include lookup of corresponding InterPro annotation in the TSV and GFF3 format | * -iprlookup: include lookup of corresponding InterPro annotation in the TSV and GFF3 format | ||
* -pa: lookup of corresponding pathway annotation | * -pa: lookup of corresponding pathway annotation | ||
* Runtime: 1min/genome, depends on applications you choose | |||
=='''Result'''== | =='''Result'''== | ||
=='''Reference'''== | =='''Reference'''== | ||
Revision as of 15:12, 9 April 2018
Introduction
Background
Functional annotation is the process of locating genes and identifying their functions (biochemical functions, regulatory functions, etc.) in the genome.
Objective
- Fully annotate 258 genomes from Gene Prediction group, focusing on antibiotic resistance
- Provide Comparative Genomics group with data required to perform Genome Wide Association Study(GWAS)
Pipeline
Tools
Prokka
Command:
prokka --outdir <output_directory> --kingdom <species' kingdom> --genus <species' genus> --gram <> --prefix <output_file> --rfam --rnammer <input_file>
- Runtime: ~ 16mins /genome
Eggnog
PilerCR
Command:
pilercr -in <input_file> -out <output_file>
- Runtime: <5 sec/genome
Phobius
Command:
phobius.pl -<output_format> <input_file> > <output_file>
- Runtime: 12-16mins /genome
LipoP
Command:
LipoP -<output_format> -<input_file> <output_file>
Runtime: ~2mins /genome
TMHMM
Command:
tmhmm -<output_format> -<input_file> <output_file>
- Runtime: ~6mins /genome
SignalP
Command:
signalp -t <organism_type> -f <output_format> <input_file>
- Runtime: ~ 4mins /genome
DeepARG
Command:
- Runtime: 3min27s /genome
Interproscan
Command:
interproscan.sh -appl <application_you_want> -iprlookup -pa -i <input_file> -f <output_format>
- -iprlookup: include lookup of corresponding InterPro annotation in the TSV and GFF3 format
- -pa: lookup of corresponding pathway annotation
- Runtime: 1min/genome, depends on applications you choose