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 m

SUBMITTER: Masella AP 

PROVIDER: S-EPMC3471323 | biostudies-literature | 2012 Feb

REPOSITORIES: biostudies-literature