Short paired-end reads trump long single-end reads for expression analysis
نویسندگان
چکیده
منابع مشابه
Inferring short tandem repeat variation from paired-end short reads
The advances of high-throughput sequencing offer an unprecedented opportunity to study genetic variation. This is challenged by the difficulty of resolving variant calls in repetitive DNA regions. We present a Bayesian method to estimate repeat-length variation from paired-end sequence read data. The method makes variant calls based on deviations in sequence fragment sizes, allowing the analysi...
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MOTIVATION Many de novo genome assemblers have been proposed recently. The basis for most existing methods relies on the de bruijn graph: a complex graph structure that attempts to encompass the entire genome. Such graphs can be prohibitively large, may fail to capture subtle information and is difficult to be parallelized. RESULT We present a method that eschews the traditional graph-based a...
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We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia stipitis. More than 95% of the genome is recovered, with no errors; half the assembled sequence is in contigs longer than 101 kilobases and in scaffolds longer...
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SUMMARY We present a program to improve haplotype reconstruction by incorporating information from paired-end reads, and demonstrate its utility on simulated data. We find that given a fixed coverage, longer reads (implying fewer of them) are preferable. AVAILABILITY The executable and user manual can be freely downloaded from ftp://ftp.sanger.ac.uk/pub/zn1/HI.
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We introduce a new data structure, a localized suffix array, based on which occurrence information is dynamically represented as the combination of global positional information and local lexicographic order information in text search applications. For the search of a pair of words within a given distance, many candidate positions that share a coarse-grained global position can be compactly rep...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2020
ISSN: 1471-2105
DOI: 10.1186/s12859-020-3484-z