J. Comput. Biol. - ComB: SNP calling and mapping analysis for color and nucleotide space platforms.

Tópicos

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{ data(1714) softwar(1251) tool(1186) }
{ featur(1941) imag(1645) propos(1176) }
{ assess(1506) score(1403) qualiti(1306) }
{ system(1050) medic(1026) inform(1018) }
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Resumo

The determination of single nucleotide polymorphisms (SNPs) has become faster and more cost effective since the advent of short read data from next generation sequencing platforms such as Roche's 454 Sequencer, Illumina's Solexa platform, and Applied Biosystems SOLiD sequencer. The SOLiD sequencing platform, which is capable of producing more than 6GB of sequence data in a single run, uses a unique encoding scheme where color reads represent transitions between adjacent nucleotides. The determination of SNPs from color reads usually involves the translation of color alignments to likely nucleotide strings to facilitate the use of tools designed for nucleotide reads. This technique results in the loss of significant information in the color read, producing many incorrect SNP calls, especially if regions exist with dense or adjacent polymorphism. Additionally, color reads align ambiguously and incorrectly more often than nucleotide reads making integrated SNP calling a difficult challenge. We have developed ComB, a SNP calling tool which operates directly in color space, using a Bayesian model to incorporate unique and ambiguous reads to iteratively determine SNP identity. ComB is capable of accurately calling short consecutive nucleotide polymorphisms and densely clustered SNPs; both of which other SNP calling tools fail to identify. ComB, which is capable of using billions of short reads to accurately and efficiently perform whole human genome SNP calling in parallel, is also capable of using sequence data or even integrating sequence and color space data sets. We use real and simulated data to demonstrate that ComB's iterative strategy and recalibration of quality scores allow it to discover more true SNPs while calling fewer false positives than tools which use only color alignments as well as tools which translate color reads to nucleotide strings.

Resumo Limpo

determin singl nucleotid polymorph snps becom faster cost effect sinc advent short read data next generat sequenc platform roch sequenc illumina solexa platform appli biosystem solid sequenc solid sequenc platform capabl produc gb sequenc data singl run use uniqu encod scheme color read repres transit adjac nucleotid determin snps color read usual involv translat color align like nucleotid string facilit use tool design nucleotid read techniqu result loss signific inform color read produc mani incorrect snp call especi region exist dens adjac polymorph addit color read align ambigu incorrect often nucleotid read make integr snp call difficult challeng develop comb snp call tool oper direct color space use bayesian model incorpor uniqu ambigu read iter determin snp ident comb capabl accur call short consecut nucleotid polymorph dens cluster snps snp call tool fail identifi comb capabl use billion short read accur effici perform whole human genom snp call parallel also capabl use sequenc data even integr sequenc color space data set use real simul data demonstr comb iter strategi recalibr qualiti score allow discov true snps call fewer fals posit tool use color align well tool translat color read nucleotid string

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