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jjmiao1314 / 16sPIP

16sPIP: A Comprehensive Analysis Pipeline for Rapid Pathogen Detection in Clinical Samples Based on 16S Metagenomic Sequencing
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Database format #4

Open ceromova opened 1 year ago

ceromova commented 1 year ago

Hello,

I would like to use your DB in another pipeline as a validation of your pipeline results. Which are the taxonomy list file and the multifasta file with all the sequences?

Thank you.

ericbrzoska commented 1 year ago

Is there an alternative tool which can be used to detect pathogens with 16s?

Best, Eric

ceromova commented 1 year ago

I am using ERVcaller and delly.

According to the previous question. Which are the taxonomy list file and the multifasta file with all the sequences?

Thank you!

ericbrzoska commented 1 year ago

I think there is no multifasta file... it looks like that all information about the species are listed via NCBI-IDs in the db folder.

Maybe those lists with NCBI-IDs could be passed into the "Choose Search Set"-Part of the website https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome

But I could not figure out what the differences between the files in the db folder are. The naming is in some cases really confusing