The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Toward almost closed genomes with GapFiller
Open accessAbstract
De novo assembly is a commonly used application of next-generation sequencing experiments. The ultimate goal is to puzzle millions of reads into one complete genome, although draft assemblies usually result in a number of gapped scaffold sequences. In this paper we propose an automated strategy, called GapFiller, to reliably close gaps within scaffolds using paired reads. The method shows good results on both bacterial and eukaryotic datasets, allowing only few errors. As a consequence, the amount of additional wetlab work needed to close a genome is drastically reduced. The software is available at http://www.baseclear.com/bioinformatics-tools/.
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Cites
The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
The sequence and de novo assembly of the giant panda genome
Li, R., Fan, W., Tian, G., Zhu, H., He, L., Cai, J., Huang, Q., Cai, Q., Li, B., Bai, Y., et al. (2010) · Nature · doi:10.1038/nature08696 · Cited by 1,180
Cited by
A human gut bacterial genome and culture collection for improved metagenomic analyses
Forster, S. C., Kumar, N., Anonye, B. O., Almeida, A., Viciani, E., Stares, M. D., Dunn, M., Mkandawire, T. T., Zhu, A., Shao, Y., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-018-0009-7 · Cited by 580
Comparative genomics of the major parasitic worms
International Helminth Genomes Consortium (2019) · Nature Genetics · doi:10.1038/s41588-018-0262-1 · Cited by 560
Xu, M., Guo, L., Gu, S., Wang, O., Zhang, R., Peters, B. A., Fan, G., Liu, X., Xu, X., Deng, L., et al. (2020) · GigaScience · doi:10.1093/gigascience/giaa094 · Cited by 482
A field guide to whole‐genome sequencing, assembly and annotation
Ekblom, R., & Wolf, J. B. W. (2014) · Evolutionary Applications · doi:10.1111/eva.12178 · Cited by 428
REAPR: a universal tool for genome assembly evaluation
Hunt, M., Kikuchi, T., Sanders, M., Newbold, C., Berriman, M., & Otto, T. D. (2013) · Genome Biology · doi:10.1186/gb-2013-14-5-r47 · Cited by 405
Metadata
- Authors
- Boetzer, M., & Pirovano, W.
- Venue
- Genome Biology
- Published
- 2012-06-25
- Volume
- 13
- Issue
- 6
- Pages
- R56-R56
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W2014286596
- Cited by
- 1,134
- References
- 4
- FWCI
- 27.18
- Type
- journal article
- Language
- en
- Open access
- gold
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