Philip Ashton, Assembly Optimisation - Impact of Error Correction and a New Assembler, SPAdes

Philip Ashton (@flashton2003 in Twitter) is a post-doctoral researcher working on bioinformatics at Public Health England. He started to write the Bits and Bugs blog in May. He is one of those rare bioinformaticians interested in genome and transcriptome assembly.

You will enjoy his new blog post, where he shows how much the assemblies improve with an error-correction step. Also, he includes SPAdes in his comparison. We have not seen many comparisons with SPAdes elsewhere apart from by GAGE and the authors of SPAdes themselves.

Maybe MaSurCA next?

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Assembly optimisation impact of error correction and a new assembler, SPAdes

We have seen significant differences between assemblies of shiga toxinigenic E. coli genomes where the DNA was extracted with different protocols. In those experiments, I used Velvet for assembly and I wanted to check whether the difference we were seeing between the different extraction methods was somehow a Velvet artefact.

The recent GAGE-B paper showed that the SPAdes assembler gave the best results at 100x coverage (N50 > 2x that of Velvet). SPAdes is a relatively new assembler, originally intended for use with single cell sequencing data that also performs well with standard data. It takes an interesting approach involving the use of paired de Bruijn graphs which allow the integration of read-pair info at a much earlier stage of assembly than most de Bruijn graph assemblers. SPAdes recommends error correction prior to assembly, BayesHammer, from the same group in St Petersburg, is bundled with SPAdes. Quake is also recommended. As an aside, SPAdes was very straightforward to install and run.

In addition to N50, assembly quality was assessed using REAPR, a reference free tool from the Sanger. We had some teething issues getting this set up but the developer, Martin Hunt, was helpful. REAPR assesses an assembly by mapping the reads to the genome and looking at whether the paired information is congruent with the assembly. It then breaks the assembly where it detects errors and returns a corrected N50. For a few samples I compared the number of misassemblies called with Quast, a reference based assembly assessment tool we have used in the past and REAPR.

So, what were the results?

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Please continue to read at his blog here.