MOESM2 of Comparative Subsequence Sets Analysis (CoSSA) is a robust approach to identify haplotype specific SNPs; mapping and pedigree analysis of a potato wart disease resistance gene Sen3
2019-05-29T05:00:00Z (GMT) by
Additional file 2. CoSSA computational requirements. Computational requirements for the biggest datasets we used in the CoSSA workflows (sequencing depth of 16 ×/haploid genome). We showed that a depth of 10 ×/haploid genome is sufficient when the parents are not sequenced and 5 ×/haploid genome when parents are sequenced which reduces these computational requirements. The different jobs were executed on the WUR Plant Breeding server. Only one node of 10.5 GB memory was used. When the jobs are parallelized for the different CoSSA samples, the reference genome dependent workflow can be run in half a day. For the reference genome independent CoSSA workflow, we advise to allocate more nodes to the reads extraction and to the de novo assembly steps as they require more time. The most time consuming step at the moment which could be improved is the script used to extract the read pairs containing the k-mers.