Sort Me RNA User Manual 2.1

• Introduction
• Installation
  • Install from tarball release
  • Install development version from git
  • Install from precompiled code
  • Uninstall
• Databases
• How to run SortMeRNA
  • Index the rRNA database: command `indexdb_rna'
    • Example 1: indexdb_rna using one database
    • Example 2: indexdb_rna using multiple databases
  • A guide to choosing `sortmerna' parameters for filtering and read mapping
  • Filter rRNA reads
    • Example 3: multiple databases and the fastest alignment option
    • Filtering paired-end reads
    • Example 4: forward-reverse paired-end reads (2 input files)
  • Read mapping
    • Mapping reads for classification
    • Example 5: mapping reads against the 16S Greengenes 97% id database with multithreading
  • OTU-picking
• SortMeRNA advanced options
• Help
• Citation