How to select the parameter "--enrichment_preset"

[jiaojiaoguan]

Dear author,

Thanks for your excellent work. I have some VLP enrichment samples from the animal gut. When I use the tool, how to select the parameter "--enrichment_preset". The default is "human", but I do not know whether I should calculate the enrichment based on the human microbiome. I hope to get your instructions.

Best Regards,
Jiaojiao

[azufre451]

Hi Jiaojiao,

Unless you have different values to provide as medians for rRNA-gene and single-copy proteins abundances, you can use the human preset.

You could also screen your specific host(s) metagenomes (i.e. unenriched standard shotgun sequencing data) against the viromeQC database, and have a more precise benchmark: in this case, you can modify the medians.csv file accordingly. The easiest way would be to change the values in the "human" column and run viromeQC with the human-preset. Happy to provide some more info if you wish!

Best,
Moreno

[jiaojiaoguan]

Hi Jiaojiao,

Unless you have different values to provide as medians for rRNA-gene and single-copy proteins abundances, you can use the human preset.

You could also screen your specific host(s) metagenomes (i.e. unenriched standard shotgun sequencing data) against the viromeQC database, and have a more precise benchmark: in this case, you can modify the medians.csv file accordingly. The easiest way would be to change the values in the "human" column and run viromeQC with the human-preset. Happy to provide some more info if you wish!

Best, Moreno

Thanks for your reply. I found that in my VLP enrichment sample, the alignment rate of LSU is large (about 30%). I am wondering whether viromeQC tool can output the alignment results for further analysis. I want to know what organism the reads are aligned.

Best,
Jiaojiao