Hello,
I am trying to assemble an insect (a leafhopper) transcriptome. The raw data is 372,756,990 reads, 150 bp in length. Previously, my lab assembled a transcriptome, using trimmed reads (using prinseq), on a local server using ABySS-PE (k=25, n=8). This assembled transcriptome contains more than 45.9 million sequences with a contig mean 58 bp and N50 59 bp, and took about 7 days to complete its assembly.
Obviously we would like to improve our assembly but it is not reasonable continue assembling on our local server (because of the amount of time it takes for each assembly).
Our lab has access to a supercomputer known as Tusker (http://hcc.unl.edu/tusker/index.php and http://hcc.unl.edu/hcccreditedit/faq.php?tp=Tusker). Tusker requires users to submit jobs using Torque (a variant of PBS) but ABySS-PE is incompatible with Torque.
So, any suggestions on a parallel program that is compatible with Torque?
Thank you very much for your help.
-Matthew
I am trying to assemble an insect (a leafhopper) transcriptome. The raw data is 372,756,990 reads, 150 bp in length. Previously, my lab assembled a transcriptome, using trimmed reads (using prinseq), on a local server using ABySS-PE (k=25, n=8). This assembled transcriptome contains more than 45.9 million sequences with a contig mean 58 bp and N50 59 bp, and took about 7 days to complete its assembly.
Obviously we would like to improve our assembly but it is not reasonable continue assembling on our local server (because of the amount of time it takes for each assembly).
Our lab has access to a supercomputer known as Tusker (http://hcc.unl.edu/tusker/index.php and http://hcc.unl.edu/hcccreditedit/faq.php?tp=Tusker). Tusker requires users to submit jobs using Torque (a variant of PBS) but ABySS-PE is incompatible with Torque.
So, any suggestions on a parallel program that is compatible with Torque?
Thank you very much for your help.
-Matthew
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