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INDEXDB_RNA(1) User Commands INDEXDB_RNA(1)

NAME

indexdb_rna - tool for filtering, mapping and OTU-picking NGS reads (indexdb)

SYNOPSIS

indexdb_rna --ref db.fasta,db.idx [OPTIONS]

DESCRIPTION

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).

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.

OPTIONS

MANDATORY OPTIONS

FASTA reference file, index file
Example:
--ref /path/to/file1.fasta,/path/to/index1
If passing multiple reference sequence files, separate them by ':'
Example:
--ref /path/f1.fasta,/path/index1:/path/f2.fasta,path/index2

OPTIONAL OPTIONS

suggested option for aligning ~99% related species (default: off)
suggested option for aligning ~75-98% related species (default: on)
directory where to write temporary files
the amount of memory (in Mbytes) for building the index (default: 3072)
seed length (default: 18)
maximum number of positions to store for each unique L-mer (default: 10000, setting --max_pos 0 will store all positions)
verbose
help
August 2015 indexdb_rna 2.0