Dataset Information

BFC: correcting Illumina sequencing errors.

ABSTRACT: BFC is a free, fast and easy-to-use sequencing error corrector designed for Illumina short reads. It uses a non-greedy algorithm but still maintains a speed comparable to implementations based on greedy methods. In evaluations on real data, BFC appears to correct more errors with fewer overcorrections in comparison to existing tools. It particularly does well in suppressing systematic sequencing errors, which helps to improve the base accuracy of de novo assemblies.https://github.com/lh3/bfchengli@broadinstitute.orgSupplementary data are available at Bioinformatics online.

SUBMITTER: Li H

PROVIDER: S-EPMC4635656 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature

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Publications

BFC: correcting Illumina sequencing errors.

Li Heng H

Bioinformatics (Oxford, England) 20150506 17

<h4>Unlabelled</h4>BFC is a free, fast and easy-to-use sequencing error corrector designed for Illumina short reads. It uses a non-greedy algorithm but still maintains a speed comparable to implementations based on greedy methods. In evaluations on real data, BFC appears to correct more errors with fewer overcorrections in comparison to existing tools. It particularly does well in suppressing systematic sequencing errors, which helps to improve the base accuracy of de novo assemblies.<h4>Availab ...[more]

PMID: 25953801

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Project description:microRNA (miRNA) expression profiles based on the highly powerful Illumina sequencing technology rely on the construction of cDNA libraries in which adaptor ligation is known to deeply favor some miRNAs over others. This introduces erroneous measurements of the miRNA abundances and relative miRNA quantities in biological samples. Here, by using the commercial miRXplore Universal Reference that contains an equimolar mixture of 963 animal miRNAs and TruSeq or bulged adaptors, we describe a method for correcting ligation biases in expression profiles obtained with standard protocols of cDNA library construction and provide data for quantifying the true miRNA abundances in biological samples. Ligation biases were evaluated at three ratios of miRNA to 3'-adaptor and four numbers of polymerase chain reaction amplification cycles by calculating efficiency captures/correcting factors for each miRNA. We show that ligation biases lead to over- or under-expression covering a 105 amplitude range. We also show that, at each miRNA:3'-adaptor ratio, coefficients of variation (CVs) of efficiency captures calculated over the four number of amplification cycles using sliding windows of 10 values ranged from 0.1 for the miRNAs of high expression to 0.6 for the miRNAs of low expression. Efficiency captures of miRNAs of high and low expression in profiles are therefore differently impacted by the number of amplification cycles. Importantly, we observed that at a given number of amplification cycles, CVs of efficiency captures calculated over the three miRNA:3'-adaptor ratios displayed a steady value of 0.3 +/- 0.05 STD for miRNAs of high and low expression. This allows, at a given number of amplification cycles, accurate comparison of miRNA expression between biological samples over a substantial expression range. Finally we provide tables of correcting factors that allow to measure the abundances of 963 miRNAs in biological samples from TruSeq-based expression profiles and, an example of their use by characterizing miRNAs of the let-7, miR-26, miR-29, and miR-30 families as the more abundant miRNAs of the rat adult cerebellum.

Dataset Information

BFC: correcting Illumina sequencing errors.

Publications

BFC: correcting Illumina sequencing errors.

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