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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
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Genome Biology

ISSN: 1474-760X

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