Question: How to extract strain genome sequence from mouse gut microbiome metagenome shotgun sequence?
gravatar for lxu12
22 months ago by
lxu120 wrote:

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

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ADD COMMENTlink modified 22 months ago by h.mon24k • written 22 months ago by lxu120
gravatar for h.mon
22 months ago by
h.mon24k wrote:

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

ADD COMMENTlink written 22 months ago by h.mon24k

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.

ADD REPLYlink written 22 months ago by lxu120
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