Peer Review #4 of "Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads (v0.3)" Article Swipe
Sparc: a sparsity-based consensus algorithm for long erroneous sequencing readsChengxi Ye, Sam Ma Motivation: The third generation sequencing (3GS) technology generates long sequences of thousands of bases.However, its current error rates are estimated in the range of 15-40%, significantly higher than those of the prevalent next generation sequencing (NGS) technologies (less than 1%).Fundamental bioinformatics tasks such as de novo genome assembly and variant calling require high quality sequences that need to be extracted from these long but erroneous 3GS sequences.Results: We describe a versatile and efficient linear complexity consensus algorithm Sparc to facilitate de novo genome assembly.Sparc builds a sparse k-mer graph using a collection of sequences from a targeted genomic region.The heaviest path which approximates the most likely genome sequence is searched through a sparsity-induced reweighted graph as the consensus sequence.Sparc supports using NGS and 3GS data together, which leads to significant improvements in both cost efficiency and computational efficiency.Experiments with Sparc show that our algorithm can efficiently provide high-quality consensus sequences using both PacBio and Oxford Nanopore sequencing technologies.With only 30x PacBio data, Sparc can reach a consensus with error rate < 0.5%.With the more challenging Oxford Nanopore data, Sparc can also achieve similar error rate when combined with NGS data.Compared with the existing approaches, Sparc[i] calculates the consensus with higher accuracy, uses 80% less memory and time, approximately.
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- Type
- peer-review
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- Landing Page
- https://doi.org/10.7287/peerj.2016v0.3/reviews/4
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All OpenAlex metadata
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https://openalex.org/W4252806746Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.7287/peerj.2016v0.3/reviews/4Digital Object Identifier
- Title
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Peer Review #4 of "Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads (v0.3)"Work title
- Type
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peer-reviewOpenAlex work type
- Language
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enPrimary language
- Publication year
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2016Year of publication
- Publication date
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2016-06-08Full publication date if available
- Authors
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Chengxi YeList of authors in order
- Landing page
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https://doi.org/10.7287/peerj.2016v0.3/reviews/4Publisher landing page
- Open access
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YesWhether a free full text is available
- OA status
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goldOpen access status per OpenAlex
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https://doi.org/10.7287/peerj.2016v0.3/reviews/4Direct OA link when available
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Computer science, AlgorithmTop concepts (fields/topics) attached by OpenAlex
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0Total citation count in OpenAlex
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19Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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