BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing

Background Advances in automated DNA sequencing technology have greatly increased the scale of genomic and metagenomic studies. An increasingly popular means of increasing project throughput is by multiplexing samples during the sequencing phase. This can be achieved by covalently linking short, uni...

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Vydané v:BMC bioinformatics Ročník 10; číslo 1; s. 362
Hlavný autor: Frank, Daniel N
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: London BioMed Central 29.10.2009
BioMed Central Ltd
Springer Nature B.V
BMC
Predmet:
Algorithms
Applications software
Base Sequence
Bioinformatics
Biomedical and Life Sciences
Computational Biology - methods
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
Computer programs
Deoxyribonucleic acid
Design
DNA
DNA Primers - chemistry
DNA sequencing
Genes
Genome
Genomics
Life Sciences
Methods
Microarrays
Microbiology
Molecular Sequence Data
Nucleotide sequence
Nucleotide sequencing
Oligonucleotide Array Sequence Analysis
Polymerase chain reaction
Primers
rRNA
Sequence Analysis, DNA - methods
Software
United States
United States > US
Colorado
Command Line
Barcoded Oligonucleotide
Ambiguous Base Call
Polished Sequence
Barcoded Primer
ISSN:1471-2105, 1471-2105
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Shrnutí:Background Advances in automated DNA sequencing technology have greatly increased the scale of genomic and metagenomic studies. An increasingly popular means of increasing project throughput is by multiplexing samples during the sequencing phase. This can be achieved by covalently linking short, unique "barcode" DNA segments to genomic DNA samples, for instance through incorporation of barcode sequences in PCR primers. Although several strategies have been described to insure that barcode sequences are unique and robust to sequencing errors, these have not been integrated into the overall primer design process, thus potentially introducing bias into PCR amplification and/or sequencing steps. Results Barcrawl is a software program that facilitates the design of barcoded primers, for multiplexed high-throughput sequencing. The program bartab can be used to deconvolute DNA sequence datasets produced by the use of multiple barcoded primers. This paper describes the functions implemented by barcrawl and bartab and presents a proof-of-concept case study of both programs in which barcoded rRNA primers were designed and validated by high-throughput sequencing. Conclusion Barcrawl and bartab can benefit researchers who are engaged in metagenomic projects that employ multiplexed specimen processing. The source code is released under the GNU general public license and can be accessed at http://www.phyloware.com .
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ISSN:1471-2105
1471-2105
DOI:10.1186/1471-2105-10-362