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