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brian-cleary / LatentStrainAnalysis

Partitioning and analysis methods for large, complex sequence datasets
MIT License
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no access to a cluster #22

Open lfaller opened 7 years ago

lfaller commented 7 years ago

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 commented 7 years ago

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!

On Tue, Jun 13, 2017 at 3:53 PM lfaller notifications@github.com 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!

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