Display Settings:

Format

Send to:

Choose Destination
See comment in PubMed Commons below
BMC Bioinformatics. 2012 Feb 14;13:31. doi: 10.1186/1471-2105-13-31.

PANDAseq: paired-end assembler for illumina sequences.

Author information

  • 1Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.

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.

PMID:
22333067
[PubMed - indexed for MEDLINE]
PMCID:
PMC3471323
Free PMC Article

Images from this publication.See all images (4)Free text

Figure 1
Figure 2
Figure 3
Figure 4
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for BioMed Central Icon for PubMed Central
    Loading ...
    Write to the Help Desk