Paper freeze

Recent developments in vg have focused on improving the mapper's performance via simulations.

As a result of this work, our simulations show that when aligning reads simulated from the 1000G variation graph, vg is equivalent to bwa mem in performance on the linear reference, and bests it considerably when aligning against the pangenome:

Experiments are completed with scripts/map-sim. The above example can be reproduced by:

vg/scripts/map-sim human.10M hs37d5.fa ref/index pan/index 32 "-s 571 -n 500000 -e 0.01 -i 0.002 -l 150 -p 500 -v 50" " "

Runtime is between 5 and 10x that of bwa mem.