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