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merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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Export splits before BAM profiling step #452

Closed dot4822 closed 7 years ago

dot4822 commented 7 years ago

Hi Meren,

I went through your tutorial and found that the 'anvi-export-splits-and-coverages' can only be used on merged database. Since the BAM profiling step takes long time, and my target is only to get splits cut up by ANVIO, I would like to know whether it is possible that you can add a new script to export fasta file of splits before BAM profiling step.

Regards, Dot

meren commented 7 years ago

(this is now resolved in the development branch and will be in the next release)

meren commented 7 years ago

Simply you will use this command to export splits instead of contigs from a single contigs database:

anvi-export-contigs -c contigs.db -o output.fa --splits-mode

:)