Minia on Raspberry Pi

In order to demonstrate the low memory footprint of Minia, a read contiger built from the GATB-core library, we experienced the implementation of this software on the Raspberry Pi computer.

The Raspberry Pi is a credit-card-sized single-board computer including an ARM1176JZF-S 700 MHz processor and 512 megabytes of RAM. Operating system and mass data storage are provided through an SD card.

C. elegans (100 Mbp) has been used as a test-bed to assemble 33 millions of 100 bp unfiltered paired-end reads (SRR065390), covering the genome at 64x. Paired-end information was not used. The following table summarizes performances and make a brief comparison with two well known software.

 

Minia

Soap de-novo

Velvet

System	Raspberry Pi	64GB Xeon E5462	64GB Xeon E5462
CPU time (hours)	18.9	6.25	13.5
Peak Memory (GB)	0.2	29.6	30.6

Number of contigs (K)	29.5	29.5	28.2
Longuest contig (Kbp)	75.2	90.9	62.6
N50 (bp)	5741	5975	6031
Sum (Mbp)	86.4	88.3	90.4

 

Reference:
G. Collet, G. Rizk, R. Chikhi, D. Lavenier, Minia on Raspberry Pi, assembling a 100 Mbp genome on a Credit Card Sized Computer, Poster at the JOBIM conference, 2013 Jul 1-4 (Toulouse) Best poster award.