Oculus: faster sequence alignment by streaming read compression
نویسندگان
چکیده
منابع مشابه
Improving PacBio Long Read Accuracy by Short Read Alignment
The recent development of third generation sequencing (TGS) generates much longer reads than second generation sequencing (SGS) and thus provides a chance to solve problems that are difficult to study through SGS alone. However, higher raw read error rates are an intrinsic drawback in most TGS technologies. Here we present a computational method, LSC, to perform error correction of TGS long rea...
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We present the Scalable Nucleotide Alignment Program (SNAP), a new short and long read aligner that is both more accurate (i.e., aligns more reads with fewer errors) and 10–100× faster than state-of-the-art tools such as BWA. Unlike recent aligners based on the Burrows-Wheeler transform, SNAP uses a simple hash index of short seed sequences from the genome, similar to BLAST’s. However, SNAP gre...
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This thesis presents an application of a generalized suffix tree extended by the use of frequency of patterns, to perform accurate and faster biological sequence analysis as an improvement on the computation time of existing tools in this area. This application utilizes the knowledge of frequency of prefixes shared by two or more sequences in a generalized suffix tree, to identify with good acc...
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New DNA sequencing technologies have achieved breakthroughs in throughput, at the expense of higher error rates. The primary way of interpreting biological sequences is via alignment, but standard alignment methods assume the sequences are accurate. Here, we describe how to incorporate the per-base error probabilities reported by sequencers into alignment. Unlike existing tools for DNA read map...
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ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2012
ISSN: 1471-2105
DOI: 10.1186/1471-2105-13-297