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how much cpu and RAM needed to assemble transcriptome by using trinity

Hello everyone,

I wanna to assemble the paired-end reads which sequenced several years ago on solexa illumina, so I need to rent server from our school's computer center. before rent I need to fill in a form in which I need to specify how much cpu, ram, hard drive space do I need, and what kind of mpi I am gonna use . I have never done this before, so I need some advice.

My raw reads are 8G in tar.gz form, and all the reads are 42472060 pairs, valid reads are 34512161 pairs, and valid reads occupy ~ 13 G hard drive space.

So how many CPU, how much RAM, storage space do I need ? what kind of MPI I am gonna use? by using that Configuration how long does it take for assembly?

trinity
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updated by Ram Ram • written by Kurban Kurban

1 answer

From trinity website :

What computing resources are required?

Ideally, you will have access to a large-memory server, roughly having ~1G of RAM per 1M reads to be assembled. The memory usage mostly depends on the complexity of the RNA-Seq data set, specifically on the number of unique k-mers. If you do not have access to a high-memory server, other freely available options are available.

How long should this take?

Trinity run-time depends on a number of factors including the number of reads to be assembled and the complexity of the transcript graphs. The assembly from start to finish can take anywhere from ~1/2 hour to 1 hour per million reads (your mileage may vary).

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updated by Ram Ram • written by Nicolas Rosewick Nicolas Rosewick

Hi @NicoBxl,

Thank you, that means I may need 60 G RAM, 20 CPU, but how much hard drive storage should I need?

Could you give me some advice on that too?

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updated by Ram Ram • written by Kurban Kurban

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