The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
BPGA- an ultra-fast pan-genome analysis pipeline
Open accessAbstract
Recent advances in ultra-high-throughput sequencing technology and metagenomics have led to a paradigm shift in microbial genomics from few genome comparisons to large-scale pan-genome studies at different scales of phylogenetic resolution. Pan-genome studies provide a framework for estimating the genomic diversity of the dataset, determining core (conserved), accessory (dispensable) and unique (strain-specific) gene pool of a species, tracing horizontal gene-flux across strains and providing insight into species evolution. The existing pan genome software tools suffer from various limitations like limited datasets, difficult installation/requirements, inadequate functional features etc. Here we present an ultra-fast computational pipeline BPGA (Bacterial Pan Genome Analysis tool) with seven functional modules. In addition to the routine pan genome analyses, BPGA introduces a number of novel features for downstream analyses like core/pan/MLST (Multi Locus Sequence Typing) phylogeny, exclusive presence/absence of genes in specific strains, subset analysis, atypical G + C content analysis and KEGG & COG mapping of core, accessory and unique genes. Other notable features include minimum running prerequisites, freedom to select the gene clustering method, ultra-fast execution, user friendly command line interface and high-quality graphics outputs. The performance of BPGA has been evaluated using a dataset of complete genome sequences of 28 Streptococcus pyogenes strains.
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Cites
Roary: rapid large-scale prokaryote pan genome analysis
Page, A. J., Cummins, C. A., Hunt, M., Wong, V. K., Reuter, S., Holden, M. T. G., Fookes, M., Falush, D., Keane, J. A., & Parkhill, J. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv421 · Cited by 5,736
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
Li, L., Stoeckert, C. J., & Roos, D. S. (2003) · Genome Research · doi:10.1101/gr.1224503 · Cited by 5,707
Pan genome of the phytoplankton Emiliania underpins its global distribution
Emiliania huxleyi Annotation Consortium, Read, B. A., Kegel, J., Klute, M. J., Kuo, A., Lefebvre, S. C., Maumus, F., Mayer, C., Miller, J., Monier, A., et al. (2013) · Nature · doi:10.1038/nature12221 · Cited by 516
Cited by
AbuOun, M., Stubberfield, E. J., Duggett, N. A., Kirchner, M., Dormer, L., Nunez-Garcia, J., Randall, L. P., Lemma, F., Crook, D. W., Teale, C., et al. (2017) · Journal of Antimicrobial Chemotherapy · doi:10.1093/jac/dkx286 · Cited by 282
Matteoli, F. P., Passarelli-Araujo, H., Pedrosa-Silva, F., Olivares, F. L., & Venancio, T. M. (2020) · Genomics · doi:10.1016/j.ygeno.2019.07.003 · Cited by 27
Genomic and functional diversity of the human-derived isolates of Faecalibacterium
Li, W., Lin, X., Liang, H., Wu, Z., Wang, M., Sun, J., Li, X., He, W., Gao, X., Hu, T., et al. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1379500 · Cited by 17
The Escherichia coli Fur pan-regulon has few conserved but many unique regulatory targets
Gao, Y., Bang, I., Seif, Y., Kim, D., & Palsson, B. O. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad253 · Cited by 14
Fatima, S., Butt, H. A., Aftab, A., & Bakhtiar, S. M. (2021) · Pakistan Journal of Biochemistry and Biotechnology · doi:10.52700/pjbb.v2i2.46 · Cited by 1
Metadata
- Authors
- Chaudhari, N. M., Gupta, V. K., & Dutta, C.
- Venue
- Scientific Reports
- Published
- 2016-04-13
- Volume
- 6
- Issue
- 1
- Pages
- 24373-24373
- ISSN
- 2045-2322 (ISSN-L)
- OpenAlex
- W2340958225
- Cited by
- 988
- References
- 3
- FWCI
- 22.27
- Type
- journal article
- Language
- en
- Open access
- gold
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