MOUNT: Seascape genomics of invertebrates in coastal Crete

Use case title (contact person)
MOUNT: Seascape genomics of invertebrates in coastal Crete (Dr. Aglaia (Cilia) Antoniou)

In-brief: description the analysis that was carried out
ddRADseq data (150bp, single read) analysis was carried out: reads were demultiplexed, quality filtered and trimmed. Five different datasets were assembled utilizing different assembly options (de novo, reference genome, reference genome + de novo, putatively coding and putatively non coding loci).

In brief: description of the pertinent project
We want to examine the population structure, the inferred populations’ connectivity and demographic history in conjunction with their dispersal capabilities and environmental parameters under a seascape genomics framework.

Comments on how the cluster supported this work
Approximately 700 million reads were processed using ipyrad. A number of nodes was used from the “batch” partition for two months (and usage is expected to continue) utilizing the job parallelization and MPI capabilities of the system where possible. A number of tools are invoked through the ipyrad pipeline hence why in certain steps all requested resources were exploited, while in others only a sole CPU is used.  Some of the larger datasets were repeatedly failing to assemble giving a number of different error messages but after a successful test run in bigmem, it turns out that memory limitation was the issue so bigmem use will be required in the future. Successful assemblies do not normally take more than 8-10 hours if given appropriate resources.

Relevant project/dataset web site if available
MOUNT (MOdern UNifying Trends in marine biology) project

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