Efficient Alignment of Illumina‐Like High‐Throughput Sequencing Reads with the GEnomic Multi‐tool (GEM) Mapper

Santiago Marco‐Sola1, Paolo Ribeca2

1 Centro Nacional de Análisis Genómico, Barcelona, 2 The Pirbright Institute, Woking
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 11.13
DOI:  10.1002/0471250953.bi1113s50
Online Posting Date:  June, 2015
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Abstract

Modern Illumina‐like high‐throughput sequencing machines allow the cheap decoding of great amounts of DNA. The GEnomic Multi‐tool (GEM) mapper is one of the fastest and most sensitive methods known to date to align such data to a known genomic reference. This unit explains how to use it effectively. © 2015 by John Wiley & Sons, Inc.

Keywords: sequencing; high‐throughput sequencing; next‐generation sequencing; bioinformatics; genomics; alignment; mapping; read mapping; sequencing read mapping

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Aligning Illumina‐Like Reads to a Reference Genome with the GEM Mapper
  • Support Protocol 1: Obtaining and Installing the GEM Package
  • Support Protocol 2: Generating a GEM Index for a Genomic Reference
  • Support Protocol 3: Converting the GEM Output to SAM
  • Guidelines for Understanding Results
  • Commentary
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
  Cock, P.J., Fields, C.J., Goto, N., Heuer, M.L., and Rice, P.M. 2010. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic. Acids Res. 38:1767‐1771.
  Derrien, T., Estellé, J., Marco, S.S., Knowles, D.G., Raineri, E., Guigó, R., and Ribeca, P. 2012. Fast computation and applications of genome mappability. PLoS One 7:e30377.
  Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078‐2079.
  Marco‐Sola, S., Sammeth, M., Guigó, R., and Ribeca, P. 2012. The GEM mapper: Fast, accurate and versatile alignment by filtration. Nat. Methods 9:1185‐1188.
  Ribeca, P. 2012. Short‐read mapping. In Bioinformatics for high‐throughput sequencing (N. Rodríguez‐Ezpeleta, M. Hackenberg and A.M. Aransay eds.) pp. 107‐125. Springer, New York.
Key Reference
  Marco‐Sola, S., Sammeth, M., Guigó, R., and Ribeca, P. 2012. The GEM mapper: Fast, accurate and versatile alignment by filtration. Nat. Methods 9:1185‐1188.
Internet Resources
  http://gemlibrary.sourceforge.net/
  The official web page where the latest releases and announcements are published.
  http://algorithms.cnag.cat/wiki/GEM:Installation_instructions
  How to install the GEM package, in detail.
  http://algorithms.cnag.cat/wiki/FAQ:The_GEM_alignment_format
  A description of the GEM alignment format.
  http://algorithms.cnag.cat/wiki/Man:gem‐indexer
  Detailed list of command line options available to program gem‐indexer.
  http://algorithms.cnag.cat/wiki/Man:gem‐mapper
  Detailed list of command line options available to program gem‐mapper.
  http://algorithms.cnag.cat/wiki/Man:gem‐2‐sam
  Detailed list of command line options available to program gem‐2‐sam.
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