Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4
For each SGB, based on the UniRef90 and UniClust90 annotations, a pangenome was generated by collecting all the UniRef/UniClust90 clusters present in at least one of the SGB’s genomes. For each cluster, the representative sequence was randomly selected within all the genomes and a coreness value was calculated based on the cluster prevalence within the 2 k highest quality genomes of the SGB. uSGBs containing less than five MAGs were discarded for the following steps.
To detect the SGB-specific marker genes, each set of core genes was then aligned against the genomes of the other SGBs using Bowtie 2 or less than 1% of the genomes of any other SGB and hitting a number of the genomes of their SGB above or equal to their coreness threshold were selected as marker genes.
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