The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit
Open accessAbstract
MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/.
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Cites
De novo assembly of human genomes with massively parallel short read sequencing
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926 · cited 1×
“06) of SOAPdenovo [19] is used.”
Self-citationToward Automatic Reconstruction of a Highly Resolved Tree of Life
Ciccarelli, F. D., Doerks, T., von Mering, C., Creevey, C. J., Snel, B., & Bork, P. (2006) · Science · doi:10.1126/science.1123061 · Cited by 1,663
Self-citationSolexaQA: 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
Cited by
An integrated catalog of reference genes in the human gut microbiome
MetaHIT Consortium, Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., Arumugam, M., Kultima, J. R., Prifti, E., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2942 · Cited by 2,164
Self-citationDisentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota
MetaHIT consortium, Forslund, K., Hildebrand, F., Nielsen, T., Falony, G., Le Chatelier, E., Sunagawa, S., Prifti, E., Vieira-Silva, S., Gudmundsdottir, V., et al. (2015) · Nature · doi:10.1038/nature15766 · Cited by 2,116
Self-citationHuman gut microbes impact host serum metabolome and insulin sensitivity
Pedersen, H. K., Gudmundsdottir, V., Nielsen, H. B., Hyotylainen, T., Nielsen, T., Jensen, B. A. H., Forslund, K., Hildebrand, F., Prifti, E., Falony, G., et al. (2016) · Nature · doi:10.1038/nature18646 · Cited by 2,116
Self-citationPotential of fecal microbiota for early-stage detection of colorectal cancer
Zeller, G., Tap, J., Voigt, A. Y., Sunagawa, S., Kultima, J. R., Costea, P. I., Amiot, A., Böhm, J., Brunetti, F., Habermann, N., et al. (2014) · Molecular Systems Biology · doi:10.15252/msb.20145645 · Cited by 1,375
Self-citationMetaHIT Consortium, Nielsen, H. B., Almeida, M., Juncker, A. S., Rasmussen, S., Li, J., Sunagawa, S., Plichta, D. R., Gautier, L., Pedersen, A. G., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2939 · Cited by 1,184
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Metadata
- Authors
- Kultima, J. R., Sunagawa, S., Li, J., Chen, W., Chen, H., Mende, D. R., Arumugam, M., Pan, Q., Liu, B., Qin, J., Wang, J., & Bork, P.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-10-17
- Volume
- 7
- Issue
- 10
- Pages
- e47656
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2041561663
- Cited by
- 199
- References
- 3
- FWCI
- 3.83
- Type
- journal article
- Language
- en
- Open access
- gold
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