The DOI matches its Crossref record; 9 of the 9 references it cites were found in a registry or an index.
Mosdepth: quick coverage calculation for genomes and exomes
Open accessAbstract
Summary: Mosdepth is a new command-line tool for rapidly calculating genome-wide sequencing coverage. It measures depth from BAM or CRAM files at either each nucleotide position in a genome or for sets of genomic regions. Genomic regions may be specified as either a BED file to evaluate coverage across capture regions, or as a fixed-size window as required for copy-number calling. Mosdepth uses a simple algorithm that is computationally efficient and enables it to quickly produce coverage summaries. We demonstrate that mosdepth is faster than existing tools and provides flexibility in the types of coverage profiles produced. Availability and implementation: mosdepth is available from https://github.com/brentp/mosdepth under the MIT license. Supplementary information: Supplementary data are available at Bioinformatics online.
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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
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
Self-citationSambamba: fast processing of NGS alignment formats
Tarasov, A., Vilella, A. J., Cuppen, E., Nijman, I. J., & Prins, P. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv098 · Cited by 2,413
BEDTools: The Swiss‐Army Tool for Genome Feature Analysis
Quinlan, A. R. (2014) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1112s47 · Cited by 2,370
Self-citationThe Simons Genome Diversity Project: 300 genomes from 142 diverse populations
Mallick, S., Li, H., Lipson, M., Mathieson, I., Gymrek, M., Racimo, F., Zhao, M., Chennagiri, N., Nordenfelt, S., Tandon, A., et al. (2016) · Nature · doi:10.1038/nature18964 · Cited by 1,584
Toward better understanding of artifacts in variant calling from high-coverage samples
Li, H. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu356 · Cited by 892
Klambauer, G., Schwarzbauer, K., Mayr, A., Clevert, D.-A., Mitterecker, A., Bodenhofer, U., & Hochreiter, S. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks003 · Cited by 455
Indexcov: fast coverage quality control for whole-genome sequencing
Pedersen, B. S., Collins, R. L., Talkowski, M. E., & Quinlan, A. R. (2017) · GigaScience · doi:10.1093/gigascience/gix090 · Cited by 47
Self-citationIndexcov: fast coverage quality control for whole-genome sequencingPreprint
Pedersen, B. S., Collins, R. L., Talkowski, M. E., & Quinlan, A. R. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/148296 · Cited by 5
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Evaluation and minimization of Cas9-independent off-target DNA editing by cytosine base editors
Doman, J. L., Raguram, A., Newby, G. A., & Liu, D. R. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0414-6 · Cited by 473
Zhou, X., Feliciano, P., Shu, C., Wang, T., Astrovskaya, I., Hall, J. B., Obiajulu, J. U., Wright, J. R., Murali, S. C., Xu, S. X., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01148-2 · Cited by 453
A complete reference genome improves analysis of human genetic variation
Aganezov, S., Yan, S. M., Soto, D. C., Kirsche, M., Zarate, S., Avdeyev, P., Taylor, D. J., Shafin, K., Shumate, A., Xiao, C., et al. (2022) · Science · doi:10.1126/science.abl3533 · Cited by 441
Metadata
- Authors
- Pedersen, B. S., & Quinlan, A. R.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-10-31
- Volume
- 34
- Issue
- 5
- Pages
- 867-868
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2950006249
- Cited by
- 1,156
- References
- 9
- FWCI
- 9.61
- Type
- journal article
- Language
- en
- Open access
- hybrid
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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