Tool:De Novo assembler (in C, supports MPI parallelism) available for experimenting with
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11 weeks ago
Graham ▴ 10

If you're the sort of person who enjoys spending an afternoon trying out and evaluating a new tool, and is comfortable compiling C code from source, have a look at https://github.com/gtoal/genelab ... I wrote this about 10 years ago but retired soon afterwards, and came across my code recently on an archive disk, so I've uploaded it to github. It might still be useful code, but it needs someone more up to date on this stuff than me to have a look at it and see if it's still useful.

I'm basically passing the code on to anyone who might find it useful - other than a little effort in handing it over, I'm not planning to get deeply into it again after 10 years of retirement! (To be quite frank I've forgotten most of the bioinformatics I had to learn in order to create the tool, working with a biologist at the time).

It can run on a single system or an MPI cluster. Subsequent to writing the documentation at that URL, I did actually run up a little cluster of 8Gb Pi4's and confirmed the code still works and does work on a cluster.

Regards,
Graham Toal gtoal@gtoal.com

de-novo trie olc • 203 views
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