The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data
Open accessAbstract
Quality control (QC) and preprocessing are essential steps for sequencing data analysis to ensure the accuracy of results. However, existing tools cannot provide a satisfying solution with integrated comprehensive functions, proper architectures, and highly scalable acceleration. In this article, we demonstrate SOAPnuke as a tool with abundant functions for a "QC-Preprocess-QC" workflow and MapReduce acceleration framework. Four modules with different preprocessing functions are designed for processing datasets from genomic, small RNA, Digital Gene Expression, and metagenomic experiments, respectively. As a workflow-like tool, SOAPnuke centralizes processing functions into 1 executable and predefines their order to avoid the necessity of reformatting different files when switching tools. Furthermore, the MapReduce framework enables large scalability to distribute all the processing works to an entire compute cluster.We conducted a benchmarking where SOAPnuke and other tools are used to preprocess a ∼30× NA12878 dataset published by GIAB. The standalone operation of SOAPnuke struck a balance between resource occupancy and performance. When accelerated on 16 working nodes with MapReduce, SOAPnuke achieved ∼5.7 times the fastest speed of other tools.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
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
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
SolexaQA: 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
Big Data: Astronomical or Genomical?
Stephens, Z. D., Lee, S. Y., Faghri, F., Campbell, R. H., Zhai, C., Efron, M. J., Iyer, R., Schatz, M. C., Sinha, S., & Robinson, G. E. (2015) · PLOS Biology · doi:10.1371/journal.pbio.1002195 · Cited by 1,340
Extensive sequencing of seven human genomes to characterize benchmark reference materials
Zook, J. M., Catoe, D., McDaniel, J., Vang, L., Spies, N., Sidow, A., Weng, Z., Liu, Y., Mason, C. E., Alexander, N., et al. (2016) · Scientific Data · doi:10.1038/sdata.2016.25 · Cited by 811 · cited 1×
“A ∼ 30 × human genome dataset published by GIAB [43] was extracted as testing data (see Additional file 4).”
Method
Cited by
fastp: an ultra-fast all-in-one FASTQ preprocessor
Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty560 · Cited by 29,721
Self-citationSingle-cell landscape of the ecosystem in early-relapse hepatocellular carcinoma
Sun, Y., Wu, L., Zhong, Y., Zhou, K., Hou, Y., Wang, Z., Zhang, Z., Xie, J., Wang, C., Chen, D., et al. (2021) · Cell · doi:10.1016/j.cell.2020.11.041 · Cited by 895
Self-citationDe novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
Hufford, M. B., Seetharam, A. S., Woodhouse, M. R., Chougule, K. M., Ou, S., Liu, J., Ricci, W. A., Guo, T., Olson, A., Qiu, Y., et al. (2021) · Science · doi:10.1126/science.abg5289 · Cited by 747
Zheng, Y., Wang, T., Tu, X., Huang, Y., Zhang, H., Tan, D., Jiang, W., Cai, S., Zhao, P., Song, R., et al. (2019) · Journal for ImmunoTherapy of Cancer · doi:10.1186/s40425-019-0650-9 · Cited by 550
Liu, S., Huang, S., Chen, F., Zhao, L., Yuan, Y., Francis, S. S., Fang, L., Li, Z., Lin, L., Liu, R., et al. (2018) · Cell · doi:10.1016/j.cell.2018.08.016 · Cited by 279
Self-citation
Metadata
- Authors
- Chen, Y., Chen, Y., Shi, C., Huang, Z., Zhang, Y., Li, S., Li, Y., Ye, J., Yu, C., Li, Z., Zhang, X., Wang, J., Yang, H., Fang, L., & Chen, Q.
- Venue
- GigaScience
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-12-04
- Volume
- 7
- Issue
- 1
- Pages
- 1-6
- ISSN
- 2047-217X (ISSN-L)
- OpenAlex
- W2774072836
- Cited by
- 2,447
- References
- 5
- FWCI
- 31.93
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. https://app.cochat.ai/papers/10.1093/gigascience/gix120
- The paper
- Chen, Y., Chen, Y., Shi, C., Huang, Z., Zhang, Y., Li, S., Li, Y., Ye, J., Yu, C., Li, Z., Zhang, X., Wang, J., Yang, H., Fang, L., & Chen, Q. (2018). SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. GigaScience. https://doi.org/10.1093/gigascience/gix120
Data sources
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.
