The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Poretools: a toolkit for analyzing nanopore sequence data
Open accessAbstract
Motivation: Nanopore sequencing may be the next disruptive technology in genomics, owing to its ability to detect single DNA molecules without prior amplification, lack of reliance on expensive optical components, and the ability to sequence long fragments. The MinION™ from Oxford Nanopore Technologies (ONT) is the first nanopore sequencer to be commercialized and is now available to early-access users. The MinION™ is a USB-connected, portable nanopore sequencer that permits real-time analysis of streaming event data. Currently, the research community lacks a standardized toolkit for the analysis of nanopore datasets. Results: We introduce poretools, a flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION™ for the purposes of quality control and downstream analysis. Poretools operates directly on the native FAST5 (an application of the HDF5 standard) file format produced by ONT and provides a wealth of format conversion utilities and data exploration and visualization tools. Availability and implementation: Poretools is an open-source software and is written in Python as both a suite of command line utilities and a Python application programming interface. Source code is freely available in Github at https://www.github.com/arq5x/poretools Contact: n.j.loman@bham.ac.uk and aaronquinlan@gmail.com Supplementary information: An IPython notebook demonstrating the functionality of poretools is in Github. Complete documentation is available at http://poretools.readthedocs.org.
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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
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Cited by
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
Afgan, E., Baker, D., Batut, B., van den Beek, M., Bouvier, D., Čech, M., Chilton, J., Clements, D., Coraor, N., Grüning, B. A., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky379 · Cited by 3,662
NanoPack: visualizing and processing long-read sequencing data
De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M., & Van Broeckhoven, C. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty149 · Cited by 3,168
The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community
Jain, M., Olsen, H. E., Paten, B., & Akeson, M. (2016) · Genome Biology · doi:10.1186/s13059-016-1103-0 · Cited by 1,588
The sequence of sequencers: The history of sequencing DNA
Heather, J. M., & Chain, B. (2016) · Genomics · doi:10.1016/j.ygeno.2015.11.003 · Cited by 1,397
“3b) [89,90], the latter of which is a small, mobile phone sized USB device, which was fi rst released to end users in an early access trial in 2014 [91].”
BackgroundByrne, A., Beaudin, A. E., Olsen, H. E., Jain, M., Cole, C., Palmer, T., DuBois, R. M., Forsberg, E. C., Akeson, M., & Vollmers, C. (2017) · Nature Communications · doi:10.1038/ncomms16027 · Cited by 379
Metadata
- Authors
- Loman, N. J., & Quinlan, A. R.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-08-20
- Volume
- 30
- Issue
- 23
- Pages
- 3399-3401
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2141040548
- Cited by
- 383
- References
- 2
- FWCI
- 17.04
- Type
- journal article
- Language
- en
- Open access
- hybrid
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