title: PANDAseq: paired-end assembler for illumina sequences.
abstract: BACKGROUND
  Illumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16S rRNA gene. Publicly available tools are needed to assemble overlapping paired-end reads while correcting mismatches and uncalled bases; many errors could be corrected to obtain higher sequence yields using quality information.
  
  
  RESULTS
  PANDAseq assembles paired-end reads rapidly and with the correction of most errors. Uncertain error corrections come from reads with many low-quality bases identified by upstream processing. Benchmarks were done using real error masks on simulated data, a pure source template, and a pooled template of genomic DNA from known organisms. PANDAseq assembled reads more rapidly and with reduced error incorporation compared to alternative methods.
  
  
  CONCLUSIONS
  PANDAseq rapidly assembles sequences and scales to billions of paired-end reads. Assembly of control libraries showed a 4-50% increase in the number of assembled sequences over naïve assembly with negligible loss of "good" sequence.
authors.affiliation: Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.
authors.forename: Andre P
authors.initials: AP
authors.lastname: Masella
authors.forename: Andrea K
authors.initials: AK
authors.lastname: Bartram
authors.forename: Jakub M
authors.initials: JM
authors.lastname: Truszkowski
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Brown
authors.forename: Josh D
authors.initials: JD
authors.lastname: Neufeld
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification*; D056186:Metagenomics; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012984:Software
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S