man sortmerna (1): tool for filtering, mapping and OTU-picking NGS reads

SYNOPSIS

sortmerna --ref db.fasta,db.idx --reads file.fa --aligned base_name_output [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
--reads STRING: FASTA/FASTQ reads file
--aligned STRING: aligned reads filepath + base file name (appropriate extension will be added)

COMMON OPTIONS

--other STRING: rejected reads filepath + base file name (appropriate extension will be added)
--fastx BOOL: output FASTA/FASTQ fil (default: off, for aligned and/or rejected reads)
--sam BOOL: output SAM alignmen (default: off, for aligned reads only)
--SQ BOOL: add SQ tags to the SAM fil (default: off)
--blast INT: output alignments in various Blast-like formats
0 - pairwise
1 - tabular (Blast -m 8 format)
2 - tabular + column for CIGAR
3 - tabular + columns for CIGAR and query coverage
--log BOOL: output overall statistic (default: off)
--num_alignments INT: report first INT alignments per read reaching E-value (default: -1, --num_alignments 0 signifies all alignments will be output)
or (default)
--best INT: report INT best alignments per read reaching E-value (default: 1) by searching --min_lis INT candidate alignments (--best 0 signifies all candidate alignments will be searched)
--min_lis INT: search all alignments having the first INT longest LIS (default: 2) LIS stands for Longest Increasing Subsequence, it is computed using seeds' positions to expand hits into longer matches prior to Smith-Waterman alignment.
--print_all_reads: output null alignment strings for non-aligned reads (default: off) to SAM and/or BLAST tabular files
--paired_in BOOL: both paired-end reads go in --aligned fasta/q file (default: off, interleaved reads only, see Section 4.2.4 of User Manual)
--paired_out BOOL: both paired-end reads go in --other fasta/q file (default: off, interleaved reads only, see Section 4.2.4 of User Manual)
--match INT: SW score (positive integer) for a match (default: 2)
--mismatch INT: SW penalty (negative integer) for a mismatch (default: -3)
--gap_open INT: SW penalty (positive integer) for introducing a gap (default: 5)
--gap_ext INT: SW penalty (positive integer) for extending a gap (default: 2)
-N INT: SW penalty for ambiguous letters (N's) (default: scored as --mismatch)
-F BOOL: search only the forward strand (default: off)
-R BOOL: search only the reverse-complementary strand (default: off)
-a INT: number of threads to use (default: 1)
-e DOUBLE: E-value threshold (default: 1)
-m INT: INT Mbytes for loading the reads into memory (default: 1024, maximum -m INT is 5872)
-v BOOL: verbose (default: off)

OTU PICKING OPTIONS

--id DOUBLE: %id similarity threshold (the alignment must still pass the E-value threshold, default: 0.97)
--coverage DOUBLE: %query coverage threshold (the alignment must still pass the E-value threshold, default: 0.97)
--de_novo_otu BOOL: FASTA/FASTQ file for reads matching database < %id
(set using --id) and < %cov (set using --coverage)
(alignment must still pass the E-value threshold, default: off)
--otu_map BOOL: output OTU map (input to QIIME's make_otu_table.py, default: off)

ADVANCED OPTIONS

see SortMeRNA user manual for more details

--passes INT: three intervals at which to place the seed on the read (L is the seed length set in indexdb_rna(1), default: L,L/2,3)
--edges INT: number (or percent if INT followed by % sign) of nucleotides to add to each edge of the read prior to SW local alignment (default: 4)
--num_seeds INT: number of seeds matched before searching for candidate LIS (default: 2)
--full_search BOOL: search for all 0-error and 1-error seed matches in the index rather than stopping after finding a 0-error match (<1% gain in sensitivity with up four-fold decrease in speed, default: off)
--pid BOOL: add pid to output file names (default: off)
-h BOOL: help
--version BOOL: SortMeRNA version number