SNIC
SUPR
SNIC SUPR
Computational time for Ellegren lab
Dnr:

SNIC 2017/1-471

Type:

SNAC Medium

Principal Investigator:

Hans Ellegren

Affiliation:

Uppsala universitet

Start Date:

2017-10-31

End Date:

2018-11-01

Primary Classification:

10609: Genetics (medical to be 30107 and agricultural to be 40402)

Webpage:

Allocation

Abstract

We are studying speciation and conservation genetics using a number of different data sources (whole genome re-sequencing with different NGS techniques, transciptome sequencing, methylation sequencing). Our main study organisms are birds (primarily flycatchers) and endangered carnivores (primarily wolves). The research is founded by the Swedish Research Council (Vetenskapsr├ądet) and Knut and Alice Wallenberg foundation. We are continuosly processing population scale datasets including mapping (bwa or STAR) and SNP calling (GATK). For the data analyzes we are using a wide range of tools, including samtools, bedtools, vcftools, rsem, htseq, selscan, SHAPEIT, paml, raxml, garli, prank, ANGSD, ADMIXTURE, beagle, LDhelmet, LUMPY, manta and plink. Our cpu usage is varying vastly from month to month (depending on where in the process each subproject is for the moment), but for 2017, our average per month (sum of all our milou projects) has been ~98,000 cpuh/month. Therefore we apply for 100,000 cpuhrs per month on rackham.