I'm trying to map short reads to a genome graph constructed from multiple whole genome alignments of A. thaliana. What is the best practice method to produce the alignments in a reasonable time frame. I've been mapping just a subset of 5000 pairs to a single chromosome graph. vg map takes >24h to complete and enormous resources (up to 500G of RAM on a single core). Mapping a full sequencig run to the full genome graph took over 7 days to complete. Any help would be appreciated. Thanks!!!
In my experience, you can use the multiple threads to speed up via the -t option: -t $nthread
where $nthread is the number of threads, e.g. 10
In this way, it will be much fast. It took me one day for 200 million paired-end reads to map to a large graph.