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NCBI-Hackathons / ViruSpy

A pipeline for viral identification from metagenomic samples
MIT License
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can't run viruspy with data not in the SRA database #1

Open pcantalupo opened 7 years ago

pcantalupo commented 7 years ago

This issue is for those who want to run viruspy against sequences that are not in the SRA database. A clear case for this is somebody that did their own sequencing and has a set of FASTQ files that they want to analyze.

DCGenomics commented 7 years ago

Magicblast can handle fastq files, so it should be relatively trivial.

Cheers!

Ben

On Sep 28, 2017 4:07 PM, "Paul Cantalupo" notifications@github.com wrote:

This issue is for those who want to run viruspy against sequences that are not in the SRA database. A clear case for this is somebody that did their own sequencing and has a set of FASTQ files that they want to analyze.

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pcantalupo commented 7 years ago

Update...added -query option support in magicblast_w_opts.sh script (802a23d0d6c45cb56b17c9717668348b45833b6a) but still need to implement the -infmt option to accept fastq files