More details regarding taxonomy DB

[aistBMRG]

Thanks for developing this tool -- I am eager to try it out.

Now, it seems that a taxonomy database is a requirement for laca init. Would it be possible to clarify the format of this database (e.g., fasta with taxonomy strings in the sequence header ...?) -- I searched for some information but could not readily find what I was looking for?

Thanks!

Dieter

[yanhui09]

You only need to define the path database_dir (where you want to place the database file) in the config.yaml. And run the workflow. It will install the database for the first use. ;)

[aistBMRG]

Thanks for the information. I will proceed accordingly.

Best.

[ramiroricardo]

You only need to define the path database_dir (where you want to place the database file) in the config.yaml. And run the workflow. It will install the database for the first use. ;)

Hi @yanhui09, I assume this will install the SILVA database? If yes, how would one run LACA with other databases, e.g. UNITE?

[yanhui09]

Hi @ramiroricardo , there're several classifier options: mmseqs, kraken and q2blast. LACA relies on the prebuilt databases from these provided classifiers.
mmseqs: no prebuilt UNITE databases according to https://mmseqs.com/latest/userguide.pdf.
kraken: no prebuilt UNITE databases according to https://benlangmead.github.io/aws-indexes/k2.
q2blast: some manual coding work need to be done according to https://forum.qiime2.org/t/how-to-train-a-unite-classifier-using-rescript/28285

laca/laca/workflow/rules/init.smk

Line 169 in 5fcefb2

qiime rescript get-silva-data \