Abstract
GapFiller, starting from a sufficiently high short reads coverage, is able to produce high coverages of accurate longer sequences (from 300 bp up to 3500 bp). The procedure to perform safe extensions, together with the mate-found check, turned out to be a powerful criterion to guarantee contigs' correctness. GapFiller has further potential, as it could be applied in a number of different scenarios, including the post-processing validation of insertions/deletions detection pipelines, pre-processing routines on datasets for de novo assembly pipelines, or in any hierarchical approach designed to assemble, analyse or validate pools of sequences.
Keywords
Computer scienceHybrid genome assemblySequence assemblyFalse positive paradoxHeuristicsAlgorithmk-merDNA sequencingData miningReference genomeComputational biologyBiologyArtificial intelligenceGenetics
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Publication Info
- Year
- 2012
- Type
- article
- Volume
- 13
- Issue
- S14
- Pages
- S8-S8
- Citations
- 356
- Access
- Closed
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Cite This
Francesca Nadalin,
Francesco Vezzi,
Alberto Policriti
(2012).
GapFiller: a de novo assembly approach to fill the gap within paired reads.
BMC Bioinformatics
, 13
(S14)
, S8-S8.
https://doi.org/10.1186/1471-2105-13-s14-s8
Identifiers
- DOI
- 10.1186/1471-2105-13-s14-s8