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CK7 / abawaca

abawaca is a binning program for metagenomics
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abawaca-build #5

Open adityabandla opened 7 years ago

adityabandla commented 7 years ago

Hi

Since, the "help" for abawaca does'nt seem to exist, requesting your help with the abawaca-build step. How does one generate the sam glob files?

If I have a depth/coverage profile, generated, say using METABAT, can I use that instead?

Best, Aditya

CK7 commented 7 years ago

Hello Aditya,

The current version of abawaca available in GitHub is still not an official one and was published as part of the publications in which it was used. I can help you with running it but I would advise that you wait with it for a few months until we publish the official version (which is going to be much better than the current one!) since the current version is not so user friendly. In the meantime I would suggest that you use other binning tools.

Best regards Itai

adityabandla commented 7 years ago

Hello Itai

Many thanks for your reply. I am giving multiple binning programs a try and hence wanted to include ABAWACA in my comparison . Though, I will wait for the official version, I would still like to give it a go and see how this preliminary version handles my data

I was able to figure out the abawaca-build command, and it generated the files, saying the run was successful. However, when I run the abawaca command, it says abawaca.links file is missing

Best, Aditya

adityabandla commented 7 years ago

Digging a bit deeper into the output files, it says /Users/ItaiSharon/dropbox/software/bin/scg.pl: No such file or directory

housw commented 6 years ago

Hi Itai,

will we have an official version soon? I would like to give it a try on a marine metagenome.

Thanks in advance. Shengwei

Handymanalan commented 6 years ago

Hi Aditya,

Would you mind sharing your script for abacawa-build? I don't know how to get the sam-glob file as well.

Cheers

Alan