How to extract strain genome sequence from mouse gut microbiome metagenome shotgun sequence?

Question

[lxu12]

Is there any tool to extract a specific strain genome from mouse gut microbiome shotgun metagenome sequence?

Answer 1

[h.mon]

If you have the sequence of the desired strain, you can do this with BBDuk.

[lxu12]

Thank you for your answer.

From heatmap and merged_abundance_table, I am interested in one strain or species. If I would check whether there is variant in the metagenome in a specific strain or species before and after treatment in mouse gut microbiome, are there any else tools? In this case, whether variant calling can be used directly, such as BWA-picard-GATK? If strain, what reference could be? Whether I can use a specific strain genome as reference? And if species, what reference could be? Many thanks.