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Name

find16S.pl - Smash wrapper for finding 16S sequences in a metagenome

Synopsis

        find16S.pl {--metagenome=<name>|--fasta-<file>} [--memory=<number>] [--db=<db>]

Options

--metagenome

name of the metagenome

--fasta

input fasta file with sequences to be classified

--memory

memory (MB) allocated for JVM (default: 4000);

--prefilter

Name of a fasta file containing (preferably) full-length 16S rDNA sequences to use as a prefilter before running the expensive HMMER search for the 16S profiles. This will make it much faster. If you do not have your own full-length 16S rDNA sequence database, you can use the one included in SMASH by specifying --prefilter=smash or just scan for 16S molecules using rrna_hmm by specifying --prefilter=rrna_hmm_only. --prefilter=smash or --prefilter=file requires WU-BLAST to be installed. (default: none)

--strict|--nostrict

Used in conjunction with --prefilter. When looking for a hit against the 16S sequence database, by default find16S.pl uses strict BLASTN parameters that look for matches over 85% or so. By specifying --nostrict, you can relax this and switch to default BLASTN parameters. (default: --strict)

--db

16S databases. Does not have an effect currently since we only use RDP.

--cpus

Number of cpus to use in the BLAST and HMMER searches. (default: 2)

--help

Prints this manual.

Description

find16S.pl can identify 16S rDNA sequences from a metagenome sample and classify them using the RDP Classifier. Since only a small fraction of metagenome sequences contain 16S rDNA, it is advisable to use the --prefilter option to speed up your search by BLASTing against a set of full-length 16S rDNA sequences. SMASH comes with such a set, and this can be used by specifying --prefilter=smash.

For classifying sequences in a 16S rDNA library, you do not have to use --prefilter since each read is expected to be a 16S rDNA sequence anyway.

POD ERRORS

Hey! The above document had some coding errors, which are explained below:

Around line 383:

You forgot a '=back' before '=head1'

Around line 394:

=back without =over

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