Question: Compute resources for running ALLPATHS-lg
gravatar for bio_d
16 months ago by
bio_d20 wrote:


I am trying a denovo assembly of a non-model reptile using ALLPATHS-lg. I have 204GB of paired-end and mate-pair data.

Since we have limited computational resources we will be applying for computational resources (e.g from XSEDE). Could anyone suggest the compute hours and disk space in terms of Service Units(S.U) that should be necessary for completing the assembly process?

Thanks in advance.

sequence assembly • 313 views
ADD COMMENTlink written 16 months ago by bio_d20

What is the expected genome size? What is the proportion of paired-end to mate-pairs, how many sizes of mate-pairs? Do you know if the genome / sample being sequenced has high polymorphism rate?

Did you check the Assemblathon paper?

ADD REPLYlink written 16 months ago by h.mon29k

The genome size is approximately 2.6G.

We have 200 bp paired-end libraries and the following sizes for mate-pair libraries: 3kB, 5.2kB, 10kB and 20kB.

Unfortunately, I have not come across the Assemblathon paper.

ADD REPLYlink written 16 months ago by bio_d20
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