.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.1.
.TH INDEXDB_RNA "1" "August 2015" "indexdb_rna 2.0" "User Commands"
.SH NAME
indexdb_rna \- tool for filtering, mapping and OTU-picking NGS reads (indexdb)
.SH SYNOPSIS
.B indexdb_rna
\fB\-\-ref\fR db.fasta,db.idx [OPTIONS]
.SH DESCRIPTION
.P
SortMeRNA is a biological sequence analysis tool for filtering, mapping and
OTU-picking NGS reads. The core algorithm is based on approximate seeds and
allows for fast and sensitive analyses of nucleotide sequences. The main
application of SortMeRNA is filtering rRNA from metatranscriptomic data.
Additional applications include OTU-picking and taxonomy assignation available
through QIIME v1.9+ (http://qiime.org - v1.9.0-rc1).
.P
SortMeRNA takes as input a file of reads (fasta or fastq format) and one or
multiple rRNA database file(s), and sorts apart rRNA and rejected reads into
two files specified by the user. Optionally, it can provide high quality local
alignments of rRNA reads against the rRNA database. SortMeRNA works with
Illumina, 454, Ion Torrent and PacBio data, and can produce SAM and
BLAST-like alignments.
.SH OPTIONS
.SS MANDATORY OPTIONS
.TP
\fB\-\-ref\fR \fISTRING,STRING\fR
FASTA reference file, index file
.br
Example:
.br
\fB\-\-ref\fR \fI\,/path/to/file1.fasta\/,/path/to/index1\fP
.br
If passing multiple reference sequence files, separate them by ':'
.br
Example:
.br
\fB\-\-ref\fR \fI/path/f1.fasta,/path/index1:/path/f2.fasta,path/index2\fP
.SS OPTIONAL OPTIONS
.TP
\fB\-\-fast\fR \fIBOOL\fR
suggested option for aligning ~99% related species (default: off)
.TP
\fB\-\-sensitive\fR \fIBOOL\fR
suggested option for aligning ~75\-98% related species (default: on)
.TP
\fB\-\-tmpdir\fR \fISTRING\fR
directory where to write temporary files
.TP
\fB\-m\fR \fIINT\fR
the amount of memory (in Mbytes) for building the index (default: 3072)
.TP
\fB\-L\fR \fIINT\fR
seed length (default: 18)
.TP
\fB\-\-max_pos\fR \fIINT\fR
maximum number of positions to store for each unique L\-mer (default: 10000,
setting \fB\-\-max_pos\fR 0 will store all positions)
.TP
\fB\-v\fR \fIBOOL\fR
verbose
.TP
\fB\-h\fR \fIBOOL\fR
help