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