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Ready Specs

All tests were performed on Dell EMC PowerEdge R940 configured as shown in Table 1. The total number of cores available in the

system is 96, and the total amount of memory is 1.5TB.

Table 1 Dell EMC PowerEdge R940 Configuration

Dell EMC PowerEdge R940

CPU

4x Intel Xeon Platinum 8168 CPU, 24c @ 2.70GHz (Skylake)

RAM

48x 32GB @2666 MHz

RHEL 7.4

Kernel

3.10.0-693.el7.x86_64

Local Storage

12x 1.2TB 10K RPM SAS 12Gbps 512n 2.5in Hot-plug Hard Drive in RAID 0

Interconnect

Intel

Omni-Path

BIOS System Profile

Performance Optimized

Logical Processor

Disabled

Virtualization Technology

Disabled

SPAdes version

3.10.1

Python version

2.7.13

The data used for the tests is a paired-end read, ERR318658 which can be downloaded from European Nucleotide Archive (ENA). The

read generated from blood sample as a control to identify somatic alterations in the primary and metastatic colorectal tumors. This data

contains 3.2 Billion Reads (BR) with the read length of 101 nucleotides.

Performance Evaluation

SPAdes runs three sets of de Bruijn graphs with 21-mer, 33-mer, and 55-mer consecutively. This is the main difference with regards to

SOAPdenovo2 which run a single k-mer, either 63-mer or 127-mer.

In Figure 2, the runtimes, wall-clock times, are plotted in days (blue bars) with various number of cores, 28, 46, and 92 cores. Since we do

not want to use the entire cores of each socket, 92 cores were picked as the maximum number of cores for the system. One core per

socket was reserved for OS and other maintenance processes. Subsequent tests were done by reducing the number of cores in half. Peak

memory consumptions for each case is plotted as a line graph. SPAdes runs significantly longer than SOAPdenovo2 due to the multiple

iterations on three different k-mers.

Figure 2 SPAdes tests with various number of cores