NAME

       indexdb_rna - tool for filtering, mapping and OTU-picking NGS reads (indexdb)

SYNOPSIS

       indexdb_rna --ref db.fasta,db.idx [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

   OPTIONAL OPTIONS
       --fast BOOL
              suggested option for aligning ~99% related species (default: off)

       --sensitive BOOL
              suggested option for aligning ~75-98% related species (default: on)

       --tmpdir STRING
              directory where to write temporary files

       -m INT the amount of memory (in Mbytes) for building the index (default: 3072)

       -L INT seed length (default: 18)

       --max_pos INT
              maximum number of positions to store for each unique L-mer (default: 10000,  setting  --max_pos  0
              will store all positions)

       -v BOOL
              verbose

       -h BOOL
              help