title: CompMap: a reference-based compression program to speed up read mapping to related reference sequences.
abstract: CONCLUSIONS
  Exhaustive mapping of next-generation sequencing data to a set of relevant reference sequences becomes an important task in pathogen discovery and metagenomic classification. However, the runtime and memory usage increase as the number of reference sequences and the repeat content among these sequences increase. In many applications, read mapping time dominates the entire application. We developed CompMap, a reference-based compression program, to speed up this process. CompMap enables the generation of a non-redundant representative sequence for the input sequences. We have demonstrated that reads can be mapped to this representative sequence with a much reduced time and memory usage, and the mapping to the original reference sequences can be recovered with high accuracy.
  
  
  METHODS
  CompMap is implemented in C and freely available at http://csse.szu.edu.cn/staff/zhuzx/CompMap/.
  
  
  BACKGROUND
  xiaoyang@broadinstitute.org
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China and Infectious Disease Initiative, The Broad Institute, Cambridge, MA 02142, USA.
authors.forename: Zexuan
authors.initials: Z
authors.lastname: Zhu
authors.affiliation: College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China and Infectious Disease Initiative, The Broad Institute, Cambridge, MA 02142, USA.
authors.forename: Linsen
authors.initials: L
authors.lastname: Li
authors.affiliation: College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China and Infectious Disease Initiative, The Broad Institute, Cambridge, MA 02142, USA.
authors.forename: Yongpeng
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China and Infectious Disease Initiative, The Broad Institute, Cambridge, MA 02142, USA.
authors.forename: Yanli
authors.initials: Y
authors.lastname: Yang
authors.affiliation: College of Computer Science and Software Engineering, Shenzhen University, Shenzhen 518060, China and Infectious Disease Initiative, The Broad Institute, Cambridge, MA 02142, USA.
authors.forename: Xiao
authors.initials: X
authors.lastname: Yang
mesh_terms: D019295:Computational Biology; D044962:Data Compression / Q000379:methods*; D015894:Genome, Human / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D012016:Reference Values; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software