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indexdb_rna - Online in the Cloud

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This is the command indexdb_rna that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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
--ref STRING,STRING
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
--fast BOOL
suggested option for aligning ~99% related species (default: off)

--sensitive BOOL
suggested option for aligning ~75-98% related species (default: on)

--tmpdir STRING
directory where to write temporary files

-m INT the amount of memory (in Mbytes) for building the index (default: 3072)

-L INT seed length (default: 18)

--max_pos INT
maximum number of positions to store for each unique L-mer (default: 10000, setting
--max_pos 0 will store all positions)

-v BOOL
verbose

-h BOOL
help

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