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DaehwanKimLab / centrifuge

Classifier for metagenomic sequences
GNU General Public License v3.0
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centrifuge-download - g option duplicated #175

Closed theo-allnutt-bioinformatics closed 4 years ago

theo-allnutt-bioinformatics commented 4 years ago

In the help section, -g option says specify program, AND download GI map. But download GI map is not implemented. How can this be done? Thanks.

mourisl commented 4 years ago

Thanks for letting us know. I've removed the -g for GI map from the usage. You can download the GI map file from ftp://ftp.ncbi.nih.gov/pub/taxonomy/ . But I'm not quite sure how Centrifuge would behave on the current gi format.

theo-allnutt-bioinformatics commented 4 years ago

Yes it does not work with the current format. It needs: accension.1 taxid. Gis do not work anymore.

On Tue, 30 Jul 2019, 10:15 Li Song, notifications@github.com wrote:

Thanks for letting us know. I've removed the -g for GI map from the usage. You can download the GI map file from ftp://ftp.ncbi.nih.gov/pub/taxonomy/ . But I'm not quite sure how Centrifuge would behave on the current gi format.

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