The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Comparison of Sequencing Utility Programs
Open accessAbstract
High throughput sequencing (HTS) has resulted in extreme growth rates of sequencing data. At our lab, we generate terabytes of data every day. It is usually seen as required for data output to be “cleaned” and processed in various ways prior to use for common tasks such as variant calling, expression quantification and assembly. Two common tasks associated with HTS are adapter trimming and paired-end joining. I have developed two tools at Expression Analysis, Inc. to address these common tasks. The names of these programs are fastq-mcf and fastq-join. I compared the performance of these tools to similar open-source utilities, both in terms of resource efficiency, and effectiveness.
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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
Cutadapt removes adapter sequences from high-throughput sequencing reads
Martin, M. (2011) · EMBnet.journal · doi:10.14806/ej.17.1.200 · Cited by 33,889
Cited by
Trimmomatic: a flexible trimmer for Illumina sequence data
Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548
Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome
Chassaing, B., Koren, O., Goodrich, J. K., Poole, A. C., Srinivasan, S., Ley, R. E., & Gewirtz, A. T. (2015) · Nature · doi:10.1038/nature14232 · Cited by 2,055
Cox, L. M., Yamanishi, S., Sohn, J., Alekseyenko, A. V., Leung, J. M., Cho, I., Kim, S. G., Li, H., Gao, Z., Mahana, D., et al. (2014) · Cell · doi:10.1016/j.cell.2014.05.052 · Cited by 1,859
Conserved cell types with divergent features in human versus mouse cortex
Hodge, R. D., Bakken, T. E., Miller, J. A., Smith, K. A., Barkan, E. R., Graybuck, L. T., Close, J. L., Long, B., Johansen, N., Penn, O., et al. (2019) · Nature · doi:10.1038/s41586-019-1506-7 · Cited by 1,775
BBMerge – Accurate paired shotgun read merging via overlap
Bushnell, B., Rood, J., & Singer, E. (2017) · PLOS ONE · doi:10.1371/journal.pone.0185056 · Cited by 1,544
Metadata
- Authors
- Aronesty, E.
- Venue
- The Open Bioinformatics Journal
- Publisher
- Bentham Science Publishers Ltd.
- Published
- 2013-01-31
- Volume
- 7
- Issue
- 1
- Pages
- 1-8
- ISSN
- 1875-0362 (ISSN-L)
- OpenAlex
- W2094100452
- Cited by
- 1,150
- References
- 2
- FWCI
- 19.50
- Type
- journal article
- Language
- en
- Open access
- diamond
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