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DaehwanKimLab / centrifuge

Classifier for metagenomic sequences
GNU General Public License v3.0
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extract matched sequences #190

Open ganiatgithub opened 4 years ago

ganiatgithub commented 4 years ago

Hi,

I'm new to centrifuge, I wanted to extract the DNA sequences from particular matches (e.g. Severe acute respiratory syndrome-related coronavirus).

I looked around a bit but seem unable to do it yet. Is there a way to extract these matches?

Many thanks!

khyox commented 4 years ago

There are different ways, but I would suggest using the script rextract from the Python package Recentrifuge, which is able to perform some downstream analysis with Centrifuge's output.