13 July 2014

I am looking for a good k-mer counter to replace the slow k-mer counting phase in fermi2. A quick survey reveals that except Jellyfish and BFCounter, most k-mer counters are disk-based, in the sense that they heavily rely on temporary files to reduce memory.

This is not a good trend in my view. In large institutions and universities with centralized computing resources, the majority of file systems are sitting over network. Network I/O is frequently slow. This is becoming even worse in the production setting when multiple instances of a tool are running at the same time and all putting heavy stress on I/O. In the end, the practical performance of disk-based tools may be far from the optimal numbers shown in the papers.

I would encourage the development of in-memory algorithms. Disks are not really a good solution to high memory.

blog comments powered by Disqus