Should SOAPdenovo2 Source Code be Made Public?

During June-July 2012, BGI made its SOAPdenovo2 executable available to the community, and we reported on how to run it in the following commentaries. Due to lack of time, we could not provide any benchmarks on how well the assembler worked compared to other assemblers.

Testing SOAPdenovo2 Pre-release Version

Testing SOAPdenovo2 Pre-release Version II (pregraph_sparse)

Testing SOAPdenovo2 Prelease Version III

Testing SOAPdenovo2 Prerelease IV (building contigs)

Testing SOAPdenovo2 Prerelease V (map and scaff)

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

Readers interested in such comparison may take a look at the SOAPdenovo2 paper that just came out at the GigaScience website. However, for a better comparison, you will have to wait for the Assemblathon 2 paper that is currently being written.

Background

There is a rapidly increasing amount of de novo genome assembly using next- generation sequencing (NGS) short reads; however, several big challenges remain to be overcome in order for this to be efficient and accurate. SOAPdenovo has been successfully applied to assemble many published genomes, but it still needs improvement in continuity, accuracy and coverage, especially in repeat regions.

Findings

To overcome these challenges, we have developed its successor, SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome.

Conclusions

Benchmark using the Assemblathon1 and GAGE datasets showed that SOAPdenovo2 greatly surpasses its predecessor SOAPdenovo and is competitive to other assemblers on both assembly length and accuracy. We also provide an updated assembly version of the 2008 Asian (YH) genome using SOAPdenovo2. Here, the contig and scaffold N50 of the YH genome were ~20.9 kbp and ~22 Mbp, respectively, which is 3-fold and 50-fold longer than the first published version. The genome coverage increased from 81.16% to 93.91%, and memory consumption was ~2/3 lower during the point of largest memory consumption.

Sbastien Boisvert, who is an expert on genome assembly, commented about lack of availability of source code of SOAPdenovo2 in his blog commentary.

The source code of SOAPdenovo2 sits in the shadows

Concern #1: ELF 64-bit LSB executables for GNU/Linux 2.6.9 are not platform- independent. Therefore, the claim of platform independence is false. For instance, I can not run these executables on OpenBSD.

Concern #2: GCC version ? 4.5.0 is not required as it is a proprietary binary distribution. Therefore this requirement is untrue.

Concern #3: proprietary software distributions are not eligible to licensing under the GNU General Public License version 3. Therefore, the authors should select their own proprietary license or release the source code of SOAPdenovo2. The previous last publicly available version was SOAPdenovo v1.05.

Peter Cock went one step further in arguing that the paper should not have been accepted given that the source code was not available.

What do you think? Is it always customary to release source code on publication of a bioinformatics paper, or is it enough to discuss the algorithm?