Identifying and characterizing bacterial strains in metagenomic samples (shotgun sequencing)
What is a bacterial strain?Family - Genus - Species - Strain A strain is a low-level taxonomic rank describing genetic variants or subtypes of a species. Theoretically, a strain lineage refers to genetically identical genomes, but practically also closely related variants are considered as the same strain. With an increasing number of mutations or acquisition of new genes (HGT) a strain can evolve in an order to be considered as a different strain.
Tools (shotgun sequencing)
identifies single nucleotide variants (SNVs) in sequenced samples compared to reference genomes to explore the variation of microbial populations → DESMAN is a co-assembly and binning approach applied across multiple samples to identifies haplotypes and the corresponding strains Read moreDiversity within species: interpreting strains in microbiomes
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