Metatrancriptomics : Pfam Database for viralVerify after rnaviralspades running

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3.5 years ago

bioAddict • 0

Hi there

I'm performing an metatranscriptomics study. I'm using rnaviralspades and in the workflow I need to use viralverify after assembling the reads with rnaviralspades. To use viralverify, this is the script provided :

   ./viralverify.py -f Input fasta file -o output_directory --hmm HMM  Path to HMM database

My question is :

For the database required for --hmm argument, should I download the whole files and directories in Pfm34.0 directory of this link : http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam34.0?

Viralverify database Pfam HMMer • 1.0k views

ADD COMMENT • link 3.5 years ago by bioAddict • 0

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Most likely you need to download and unpack only this file:

http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam34.0/Pfam-A.hmm.gz

ADD REPLY • link 3.5 years ago by Mensur Dlakic ★ 28k

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Thank you very much

ADD REPLY • link 3.5 years ago by bioAddict • 0

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