Open Access Highly Accessed Software

PANDAseq: paired-end assembler for illumina sequences

Andre P Masella1, Andrea K Bartram1, Jakub M Truszkowski2, Daniel G Brown2 and Josh D Neufeld1*

Author affiliations

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

2 David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, Ontario, Canada

For all author emails, please log on.

Citation and License

BMC Bioinformatics 2012, 13:31  doi:10.1186/1471-2105-13-31

Published: 14 February 2012



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.


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.


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.