Table 3.

Comparison of alignment methods using 10M single-end 101-bp reads from individual NA12878 (SRR622457)

Method	Index size	Memory usage	CPU time
Bowtie 2-GRCh38	3.9G	3.3G	1.00x (73m)
RandFlow-LD	23.3G	3.3G	2.04x (149m)
RandFlow-LD-26	104.9G	3.3G	5.89x (430m)
vg	25.4G	25.6G	11.26x (822m)

The vg index includes variants with allele frequency ≥ 10% in the 1000-Genomes Project GRCh38 call set. The RandFlow-LD indexes include the indexes for liftover and Bowtie 2 indexes for the global major-allele reference as well as second-pass population references. CPU time is compared to a baseline run of Bowtie 2 to the GRCh38 primary assembly