PANDAseq: paired-end assembler for illumina sequences.

BMC Bioinformatics
Andre P MasellaJosh D Neufeld

Abstract

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.

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Datasets Mentioned

BETA
SRA024100

Methods Mentioned

BETA
PCR
Illumina sequencing
used
for

Software Mentioned

iTags
Windows
Linux
PANDAseq
MacOS
BIPES
Illumina
PHRAP
SHERA
CASAVA

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