title: RAMBO-K: Rapid and Sensitive Removal of Background Sequences from Next Generation Sequencing Data.
abstract: BACKGROUND
  The assembly of viral or endosymbiont genomes from Next Generation Sequencing (NGS) data is often hampered by the predominant abundance of reads originating from the host organism. These reads increase the memory and CPU time usage of the assembler and can lead to misassemblies.
  
  
  RESULTS
  We developed RAMBO-K (Read Assignment Method Based On K-mers), a tool which allows rapid and sensitive removal of unwanted host sequences from NGS datasets. Reaching a speed of 10 Megabases/s on 4 CPU cores and a standard hard drive, RAMBO-K is faster than any tool we tested, while showing a consistently high sensitivity and specificity across different datasets.
  
  
  CONCLUSIONS
  RAMBO-K rapidly and reliably separates reads from different species without data preprocessing. It is suitable as a straightforward standard solution for workflows dealing with mixed datasets. Binaries and source code (java and python) are available from http://sourceforge.net/projects/rambok/.
authors.affiliation: Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353, Berlin, Germany.
authors.forename: Simon H
authors.initials: SH
authors.lastname: Tausch
authors.affiliation: Research Group Bioinformatics (NG4), Robert Koch Institute, 13353, Berlin, Germany.
authors.forename: Bernhard Y
authors.initials: BY
authors.lastname: Renard
authors.affiliation: Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353, Berlin, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Nitsche
authors.affiliation: Centre for Biological Threats and Special Pathogens, Robert Koch Institute, 13353, Berlin, Germany; Research Group Bioinformatics (NG4), Robert Koch Institute, 13353, Berlin, Germany.
authors.forename: Piotr Wojciech
authors.initials: PW
authors.lastname: Dabrowski
mesh_terms: D000465:Algorithms; D066264:Datasets as Topic; D016678:Genome / Q000235:genetics; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D011381:Programming Languages; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software