Welcome to the Novoalign User Guide

These pages will look at some of the uses of Novoalign and options that are suitable for each type of sequencing. We will also look at performance issues and how you can use options to improve performance.

If you would like to contribute to this Wiki we would be pleased to add you as an Editor, just drop us an email with your request. Or else just send us your content and we'll add it.

Contents:

• Getting Started
• Adapter Stripping
  • 3 Prime Adapter Stripping
  • Paired End Short Fragment Detection and Adapter Stripping
  • PCR Adapter Stripping
• Micro RNA
• RNASeq analysis: mRNA and the Spliceosome
• Bisulphite treated reads
  • Novomethyl - Analyzing Methylation Status
  • Regard the Bisulphite Treatment
• Performance Notes
  • Long Single End Reads
  • Short vs Long Reads
  • HPCs
• Quality Calibration
  • Bisulphite Treated DNA
  • The phiX Lane
  • Streptococcus suis Quality Calibration
• Novoalign Command Line Options
  • Reporting Multiple Alignments per Read
  • Paired Read Modes