Our MEGAHIT review

It may not surprise peope to learn that I was one of the reviewers on the MEGAHIT metagenome assembly paper... which is now published!.

Below is my review, edited to remove all of the stuff they addressed in their revision.

Please also see our first blog post on MEGAHIT and Adam Rivers' blog post on metatranscriptome assembly with MEGAHIT, too!

It's worth noting that the evaluation I did for the first blog post was used in the final paper ;). Successful adventures in peer review!

Li et al describe a new approach to metagenome assembly and provide an implementation of this approach in the MEGAHIT software. The new approach constructs a succinct de Bruijn graph using multiple k-mers, and uses a novel "mercy k-mer" approach that preserves low-abundance regions of reads. They also use GPUs to accelerate the graph construction.

The paper reads well. The "mercy k-mer" approach is novel to my knowledge, but makes intuitive sense. The GPU implementation seems to yield a significant improvement (although we did not test it). The software is available, licensed under GPL, is fairly straightforward to compile, and runs cleanly. In our hands, it produced good results on known datasets and ran extraordinarily fast and in low memory (see below). The authors are to be commended on all of this!

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See http://ivory.idyll.org/blog/2014-how-good-is-megahit.html for a blog post on the evaluation we did. The authors should feel free to take our makefile & results and build off of them; it's all under BSD license.

In sum, I find this to be a great piece of software, with good algorithmic insights, good implementation (at least from a cursory usage), and lots of promise.


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