sortmerna - Online in the Cloud

PROGRAM:

NAME

sortmerna - 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

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