SOPRA: Scaffolding algorithm for paired reads via statistical optimization
نویسندگان
چکیده
منابع مشابه
statistical inference via empirical bayes approach for stationary and dynamic contingency tables
چکیده ندارد.
15 صفحه اولSCARPA: scaffolding reads with practical algorithms
MOTIVATION Scaffolding is the process of ordering and orienting contigs produced during genome assembly. Accurate scaffolding is essential for finishing draft assemblies, as it facilitates the costly and laborious procedures needed to fill in the gaps between contigs. Conventional formulations of the scaffolding problem are intractable, and most scaffolding programs rely on heuristic or approxi...
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Motivation Sequencing of human genomes is now routine, and assembly of shotgun reads is increasingly feasible. However, assemblies often fail to inform about chromosome-scale structure due to a lack of linkage information over long stretches of DNA-a shortcoming that is being addressed by new sequencing protocols, such as the GemCode and Chromium linked reads from 10 × Genomics. Results Here,...
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random-permutations-based algorithm is presented for alignment of long paired-end reads. An implementation of the algorithm is shown to process a million pairs of 100 − 500bp-long reads in 3-10 minutes on a single CPU, correctly aligning more reads than popular fast aligners, 5-100 times faster. Approved for public release: distribution is unlimited.
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In this work we present a significance curve to segregate random alignments from true matches in by identity sequence comparison, especially suitable for sequencing data produced by NGS-technologies. The experimental approach reproduces the random local ungapped similarities distribution by score and length from which it is possible to asses the statistical significance of any particular ungapp...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2010
ISSN: 1471-2105
DOI: 10.1186/1471-2105-11-345