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Table 3 Comparison of alignment methods using 10M single-end 101-bp reads from individual NA12878 (SRR622457)

From: Reference flow: reducing reference bias using multiple population genomes

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)
  1. 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