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