no access to a cluster

[lfaller]

Dear Dr. Cleary,

I would like to try your software on a metagenomics dataset but I don't currently have access to a cluster.

I have paired-end reads for seven samples that total about 346 million read pairs (42 Gigabytes of fastq files).

I have access to a multi-core machine with 250 Gb of memory and 40 cores, or I could use a large AWS instance.

Would either of these machines work to run your LSA algorithm?

Thanks for any advice!

[brian-cleary]

Hi, Thanks for the interest! Yes - you could give this a try on a single machine by following the steps detailed for running the test data: https://latentstrainanalysis.readthedocs.io/en/latest/getting_started.html Set your directories up in the same way they are set up for the test data. In "original_reads/" you'll replace the test data files with your own, paying particular attention to the following: "Note that there is one file per sample, that mate pairs are interleaved, and that files are named sample_id.*.fastq." I hope this helps!

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On Tue, Jun 13, 2017 at 3:53 PM lfaller ***@***.***> wrote: Dear Dr. Cleary, I would like to try your software on a metagenomics dataset but I don't currently have access to a cluster. I have paired-end reads for seven samples that total about 346 million read pairs (42 Gigabytes of fastq files). I have access to a multi-core machine with 250 Gb of memory and 40 cores, or I could use a large AWS instance. Would either of these machines work to run your LSA algorithm? Thanks for any advice! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#22>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ACLD5sRi4gTxQO7D0EV0jDXjEMTBfpUkks5sDuiegaJpZM4N5ABI> .