NGmerge: Merging paired-end reads via novel empirically-derived models of sequencing errors
BMC Bioinformatics, ISSN: 1471-2105, Vol: 19, Issue: 1, Page: 536
2018
- 134Citations
- 170Captures
- 1Mentions
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Example: if you select the 1-year option for an article published in 2019 and a metric category shows 90%, that means that the article or review is performing better than 90% of the other articles/reviews published in that journal in 2019. If you select the 3-year option for the same article published in 2019 and the metric category shows 90%, that means that the article or review is performing better than 90% of the other articles/reviews published in that journal in 2019, 2018 and 2017.
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Example: if you select the 1-year option for an article published in 2019 and a metric category shows 90%, that means that the article or review is performing better than 90% of the other articles/reviews published in that journal in 2019. If you select the 3-year option for the same article published in 2019 and the metric category shows 90%, that means that the article or review is performing better than 90% of the other articles/reviews published in that journal in 2019, 2018 and 2017.
Citation Benchmarking is provided by Scopus and SciVal and is different from the metrics context provided by PlumX Metrics.
Metrics Details
- Citations134
- Citation Indexes133
- 133
- CrossRef4
- Patent Family Citations1
- 1
- Captures170
- Readers170
- 166
- Mentions1
- News Mentions1
- 1
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Article Description
Background: Advances in Illumina DNA sequencing technology have produced longer paired-end reads that increasingly have sequence overlaps. These reads can be merged into a single read that spans the full length of the original DNA fragment, allowing for error correction and accurate determination of read coverage. Extant merging programs utilize simplistic or unverified models for the selection of bases and quality scores for the overlapping region of merged reads. Results: We first examined the baseline quality score - error rate relationship using sequence reads derived from PhiX. In contrast to numerous published reports, we found that the quality scores produced by Illumina were not substantially inflated above the theoretical values, once the reference genome was corrected for unreported sequence variants. The PhiX reads were then used to create empirical models of sequencing errors in overlapping regions of paired-end reads, and these models were incorporated into a novel merging program, NGmerge. We demonstrate that NGmerge corrects errors and ambiguous bases better than other merging programs, and that it assigns quality scores for merged bases that accurately reflect the error rates. Our results also show that, contrary to published analyses, the sequencing errors of paired-end reads are not independent. Conclusions: We provide a free and open-source program, NGmerge, that performs better than existing read merging programs. NGmerge is available on GitHub ( https://github.com/harvardinformatics/NGmerge ) under the MIT License; it is written in C and supported on Linux.
Bibliographic Details
http://www.scopus.com/inward/record.url?partnerID=HzOxMe3b&scp=85058925102&origin=inward; http://dx.doi.org/10.1186/s12859-018-2579-2; http://www.ncbi.nlm.nih.gov/pubmed/30572828; https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2579-2; https://dx.doi.org/10.1186/s12859-018-2579-2
Springer Science and Business Media LLC
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