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Ready Solutions Engineering Test Results

the property of their respective owners. Published in the USA. Dell EMC believes the information in this document is accurate as of its publication date. The information is

subject to change without notice.

De Novo Assembly with SPAdes assembler

Overview

We published the whitepaper, “Dell EMC PowerEdge R940 makes De Novo Aseembly easier”, last year to study the behavior of

SOAPdenovo2 [1]. However, the whitepaper is limited to one De Novo assembly application. Hence, we want to expand our application

coverage little further. We decided to test SPAdes (2012) since it is a relatively new application and reported for some improvement on

the Euler-Velvet-SC assembler (2011) and SOAPdenovo

. SPAdes is also based on de Bruijn graph algorithm like most of the

assemblers targeting Next Generation Sequencing (NGS) data. De Bruijin graph-based assemblers would be more appropriate for

larger datasets having more than a hundred-millions of short reads.

As shown in Figure 1, Greedy-Extension and overlap-layout-consensus (OLC) approaches were used in the very early next gen

assemblers [2]. Greedy-Extension’s heuristic is that the highest scoring alignment takes on another read with the highest score.

However, this approach is vulnerable to imperfect overlaps and multiple matches among the reads and leads to an incomplete

assembly or an arrested assembly. OLC approach works better for long reads such as Sanger or other technology generating more

than 100bp due to minimum overlap threshold (454, Ion Torrent, PacBio, and so on). De Bruijin graph-based assemblers are more

suitable for short read sequencing technologies such as Illumina. The approach breaks the sequencing reads into successive k-mers,

and the graph maps the k-mers. Each k-mer forms a node, and edges are drawn between each k-mer in a read.

SPAdes is a relatively recent application based on de Bruijn graph for both single-cell and multicell data. It improves on the recently

released Euler Velvet Single Cell (E +V- SC) assembler (specialized for single-cell data) and on popular assemblers Velvet and

SoapDeNovo (for multicell data).

Figure 1 Overview of de novo short reads assemblers.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3056720/

Summary of content (3 pages)

PAGE 1
Ready Solutions Engineering Test Results 1 De Novo Assembly with SPAdes assembler Overview We published the whitepaper, “Dell EMC PowerEdge R940 makes De Novo Aseembly easier”, last year to study the behavior of SOAPdenovo2 [1]. However, the whitepaper is limited to one De Novo assembly application. Hence, we want to expand our application coverage little further.
PAGE 2
Ready Specs 2 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 CPU RAM OS Kernel Local Storage Interconnect BIOS System Profile Logical Processor Virtualization Technology SPAdes version Python version Dell EMC PowerEdge R940 4x Intel Xeon Platinum 8168 CPU, 24c @ 2.70GHz (Skylake) 48x 32GB @2666 MHz RHEL 7.4 3.10.0-693.el7.
PAGE 3
Ready Specs 3 The peak memory consumption is very similar to SOAPdenovo2. Both applications require slightly less than 800GB memory to process 3.2 BR. Conclusion Utilizing more cores helps to reduce the runtime of SPAdes significantly as shown in Figure 2. For SPAdes, it is recommendable to use the highest core count CPUs like Intel Xeon Plantinum 8180 processor with 28 cores and 3.80GHz to bring down the runtime further. Resources Internal web page 1. http://en.community.dell.