The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
AlienTrimmer: A tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads
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Citations
Cites
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
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439
Quail, M., Smith, M. E., Coupland, P., Otto, T. D., Harris, S. R., Connor, T. R., Bertoni, A., Swerdlow, H. P., & Gu, Y. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-341 · Cited by 2,031 · cited 2×
“Ion reads were supported by low Phred quality scores on average (for more details, see [19]), we selected a quality cut-off of 13 for this dataset, in order to not discard too many reads.”
MethodSolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data
Cox, M. P., Peterson, D. A., & Biggs, P. J. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-485 · Cited by 1,357
Research works printed but not linked: 14
- Lindgreen, 2012, AdapterRemoval: easy cleaning of next-generation sequencing reads, BMC Res. Notes, 5, 337, 10.1186/1756-0500-5-337 · DOI · Paper page
- Dodt, 2012, FLEXBAR—flexible barcode and adapter processing for next-generation sequencing platforms, Biology, 1, 895, 10.3390/biology1030895 · DOI · Paper page
- Kong, 2011, Btrim: a fast, lightweight adapter and quality trimming program for next-generation sequencing technologies, Genomics, 98, 152, 10.1016/j.ygeno.2011.05.009 · DOI · Paper page
- Li, 2009, Fast and accurate short read alignment with Burrows–Wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324 · DOI · Paper page
- Li, 2009, The sequence alignment/map (SAM) format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352 · DOI · Paper page
- Miller, 2010, Assembly algorithms for next-generation sequencing data, Genomics, 95, 315, 10.1016/j.ygeno.2010.03.001 · DOI · Paper page
- Swets, 2000, Better decision through science, Sci. Am., 283, 82, 10.1038/scientificamerican1000-82 · DOI · Paper page
- Hanley, 1982, The meaning and use of the area under a receiver operating characteristic (ROC) curve, Radiology, 143, 29, 10.1148/radiology.143.1.7063747 · DOI · Paper page
- Nakamura, 2011, Sequence-specific error profile of Illumina sequencers, Nucleic Acids Res., 39, e90, 10.1093/nar/gkr344 · DOI · Paper page
- Smeds, 2011, ConDeTri — a content dependent read trimmer for Illumina data, PLoS One, 6, e26314, 10.1371/journal.pone.0026314 · DOI · Paper page
- Minoche, 2011, Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems, Genome Biol., 12, R112, 10.1186/gb-2011-12-11-r112 · DOI · Paper page
- Yu, 2012, How do alignment programs perform on sequencing data with varying qualities and from repetitive regions?, BioData Min., 5, 6, 10.1186/1756-0381-5-6 · DOI
- Cock, 2009, The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants, Nucleic Acids Res., 38, 1767, 10.1093/nar/gkp1137 · DOI · Paper page
- Knuth, 1973, vol. 3
Cited by
Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors
Routy, B., Le Chatelier, E., Derosa, L., Duong, C. P. M., Alou, M. T., Daillère, R., Fluckiger, A., Messaoudene, M., Rauber, C., Roberti, M. P., et al. (2018) · Science · doi:10.1126/science.aan3706 · Cited by 5,671
Whole genome-based population biology and epidemiological surveillance of Listeria monocytogenes
Moura, A., Criscuolo, A., Pouseele, H., Maury, M. M., Leclercq, A., Tarr, C., Björkman, J. T., Dallman, T., Reimer, A., Enouf, V., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.185 · Cited by 668
Self-citationIntestinal microbiota influences clinical outcome and side effects of early breast cancer treatment
Terrisse, S., Derosa, L., Iebba, V., Ghiringhelli, F., Vaz-Luis, I., Kroemer, G., Fidelle, M., Christodoulidis, S., Segata, N., Thomas, A. M., et al. (2021) · Cell Death & Differentiation · doi:10.1038/s41418-021-00784-1 · Cited by 172
Tonneau, M., Nolin-Lapalme, A., Kazandjian, S., Auclin, E., Panasci, J., Benlaifaoui, M., Ponce, M., Al-Saleh, A., Belkaid, W., Naimi, S., et al. (2022) · OncoImmunology · doi:10.1080/2162402x.2022.2096535 · Cited by 34
Metadata
- Authors
- Criscuolo, A., & Brisse, S.
- Venue
- Genomics
- Publisher
- Elsevier BV
- Published
- 2013-11
- Volume
- 102
- Issue
- 5-6
- Pages
- 500-506
- ISSN
- 0888-7543 (ISSN-L)
- OpenAlex
- W2007703905
- Cited by
- 241
- References
- 4
- FWCI
- 2.82
- Type
- journal article
- Language
- en
- Open access
- bronze
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 546 d)
- Funders
- Région Ile-de-France
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- CoChat. (2026). Citation check: AlienTrimmer: A tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads. https://app.cochat.ai/papers/10.1016/j.ygeno.2013.07.011
- The paper
- Criscuolo, A., & Brisse, S. (2013). AlienTrimmer: A tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads. Genomics. https://doi.org/10.1016/j.ygeno.2013.07.011
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
