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MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun metagenomic data [article]

Florian Plaza Oñate, Emmanuelle Le Chatelier, Mathieu Almeida, Alessandra C. L. Cervino, Franck Gauthier, Frédéric Magoulès, S. Dusko Ehrlich, Matthieu Pichaud
2017 bioRxiv   pre-print
Results: We introduce MSPminer, a computationally efficient software tool that reconstitutes Meta-genomic Species Pan-genomes (MSPs) by binning co-abundant genes across metagenomic samples.  ...  Motivation: Analysis toolkits for shotgun metagenomic data achieve strain-level characterization of complex microbial communities by capturing intra-species gene content variation.  ...  Conflict of Interest: none declared.  ... 
doi:10.1101/173203 fatcat:qzmquyfxffd7biydlvefp2fymm

Integrating pan-genome with metagenome for microbial community profiling

Chaofang Zhong, Chaoyun Chen, Lusheng Wang, Kang Ning
2021 Computational and Structural Biotechnology Journal  
Combining pan-genome and metagenome analysis can reveal the microbial complicated connections from an individual complete genome to a mixture of genomes, thereby extending the catalog of traditional individual  ...  This review summarized the pan-genome and metagenome approaches, the combined strategies of pan-genome and metagenome, and applications of these combined strategies in studies of microbial dynamics, evolution  ...  This pan-genome based metagenome approach is reference-free to bin co-abundant genes and reconstitute cross- community pan-genomes.  ... 
doi:10.1016/j.csbj.2021.02.021 pmid:33841754 pmcid:PMC8010324 fatcat:cy6ub5uvwrcx3j3bor7uy4wovu