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Sanity check with various assemblers' output #216

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fedarko opened this issue Feb 22, 2022 · 0 comments
Open

Sanity check with various assemblers' output #216

fedarko opened this issue Feb 22, 2022 · 0 comments
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administrative Usually non-code-related issues we need to take care of documentation

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@fedarko
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fedarko commented Feb 22, 2022

In #215, I added a fancy table showing the input filetypes supported by MetagenomeScope. Since most assemblers can output GFA / FASTG files, it would be good to list some of these assemblers in this table (... to indicate to users of these assemblers that "yes you can use MetagenomeScope with your data!")

However, I'm not about to list a zillion assemblers here only to find out that their GFA files are actually subtly incompatible with MetagenomeScope or whatever. So it would be good to take some time and briefly sanity check the output of some assemblers to verify that these assemblers are compatible with MetagenomeScope.

This is primarily an issue with FASTG files, since the "dialect" accepted by MetagenomeScope differs from the ordinary FASTG "dialect". (It's a long story.)

Anyway, going through and briefly checking that assemblers' outputs look good isn't a perfect solution, since of course these tools, filetypes, etc. will continue to evolve outside of our control -- this table will inevitably become outdated someday. But we can at least try to make it correct for the time being.

@fedarko fedarko added administrative Usually non-code-related issues we need to take care of documentation labels Feb 22, 2022
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