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HingeAssembler / HINGE

Software accompanying "HINGE: Long-Read Assembly Achieves Optimal Repeat Resolution"
http://genome.cshlp.org/content/27/5/747.full.pdf+html?sid=39918b0d-7a7d-4a12-b720-9238834902fd
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hinge on a large plant genome #156

Open dcopetti opened 5 years ago

dcopetti commented 5 years ago

Hello, we have ~30x coverage ONT (N50 9.3 kb, 165 Gb) of a ~5 Gb plant genome and we would like to assemble it with HINGE - we wonder if recently the updates make it possible to handle such genomes. To run it on a cluster, we also need to estimate the resources needed: do you think that 1 TB memory will be enough? will 60-100 cores be enough to run the assembly in a decent time? (is it possible to get an estimated assembly time?) Also, how much storage space do you think we will need? Would 4 TB be enough to write intermediate files? Lastly, is the I/O speed of any importance at any step? We wonder if you can tell us how to guestimate how many resources to allocate in our case. Thanks, Dario

alimayy commented 5 years ago

I suggest waiting for the answer of developers but I’m not sure if Hinge, which is designed for bacterial genomes, is the best option for you. I strongly suggest looking into the TULIP assembler