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motu-tool / mOTUs

motus - a tool for marker gene-based OTU (mOTU) profiling
GNU General Public License v3.0
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profiling contigs over reads? #22

Closed raw937 closed 5 years ago

raw937 commented 5 years ago

Hello,

Is it possible to profile contigs over reads?

AlessioMilanese commented 5 years ago

Hi @raw937,

Not really. We are mapping reads using bwa, which is designed for short reads. Check out: https://github.com/AlessioMilanese/classify-genomes

Do you have contigs or metagenome-assembled genomes?

raw937 commented 5 years ago

Thanks for this!

I have good genome bins. This very helpful. I am trying to find a way to convert the long contigs (>5k) into mOTUs that aren't binning well.

raw937 commented 5 years ago

This is a cool tool "classify-genomes." I can't get the databases to download.

 python setup.py 
 ------------------------------------------------------------------------------
|                           SETUP CLASSIFY-GENOMES                             |
 ------------------------------------------------------------------------------
Download the compressed motus database (~1Gb)
 954997496  [100.00%]

Check md5: MD5 verified
Extract files from the archive...Error: failed to extract files

I tried to copy from mOTU_v2 no success.

AlessioMilanese commented 5 years ago

Looking at https://github.com/AlessioMilanese/classify-genomes/issues/1

it's because you exceed your disk quota. You need ~1Gb of free space.

AlessioMilanese commented 5 years ago

Issue solved in https://github.com/AlessioMilanese/classify-genomes/issues/1