Provided by: sortmerna_2.1-3_amd64
sortmerna - tool for filtering, mapping and OTU-picking NGS reads
sortmerna --ref db.fasta,db.idx --reads file.fa --aligned base_name_output [OPTIONS]
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.
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