article Open AccessTop 1% cited
PANDAseq: paired-end assembler for illumina sequences
BMC Bioinformatics · 2012 · Vol. 13(1) · pp. 31–31
Andre Masella✉(University of Waterloo)Andrea K. Bartram(University of Waterloo)Jakub Truszkowski(University of Waterloo)Daniel G. Brown(University of Waterloo)Josh D. Neufeld(University of Waterloo)
Abstract
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.
Genomics and Phylogenetic StudiesMicrobial Community Ecology and PhysiologyBacterial Genetics and BiotechnologyAmpliconComputer scienceSequence (biology)Error detection and correctionk-merAmplicon sequencingSequence assemblyComputational biologyDNA sequencingBiology
MeSH terms
BacteriaRNA, BacterialRNA, Ribosomal, 16SSoftwareMetagenomics
Funding
- Government of Ontario
- Natural Sciences and Engineering Research Council of Canada
Citations
2,205
FWCI
25.77
field-weighted impact
References
12
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100%
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References
A general method applicable to the search for similarities in the amino acid sequence of two proteins
Journal of Molecular Biology · 1970 · 11,386 citations
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
Proceedings of the National Academy of Sciences · 2010 · 9,826 citations
Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
Applied and Environmental Microbiology · 1993 · 11,416 citations
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Bioinformatics · 2006 · 11,865 citations
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