Table of Contents

• Basic short read mapping
• Exome sequencing analysis
• SNP and MicroIndel detection
• microRNA mapping
• Novoalign SAM format validation
• Mapping reads with Cluster-Aware NovoalignMPI
• Demultiplexing barcoded/indexed reads with Novobarcode
• Extracting unmapped reads from a BAM file produced by novoalign

Introduction

Novoalign and NovoalignCS are highly accurate programs for mapping next-generation sequencing reads to a reference database. The purpose of this guide is to provide quick, usable examples for everyday scenarios of working with short read data and aligning these to a reference genome sequence database.
For more in-depth understanding of the various options available please consult the Novoalign & NovoalignCS reference manual available from our free Downloads area.
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Dependencies

Ensure that you have these executables in your $PATH environment variable

1. Novocraft alignment suite (novoalign, novoalignCS, novoalignMPI, novobarcode, novoindex,etc).
2. BedTools command line programs.
3. Samtools version 0.1.8 or highter command line programs.
4. Picard java command line programs
5. Genome Analysis Toolkit java programs.

References

1. Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 1950594]
2. Quinlan, AR and Hall, IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.
3. The Picard library. http://picard.sf.net
4. The Genome Analysis toolkit. http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit.