Compression of Next-generation Sequencing Reads Aided by Highly Efficient de novo Assembly


A month back, we presented a commentary on Quip, Minia, SlimGene and Titus Browns paper on Scaling Metagenome. We just found out that the Quip paper is out in Nucleic Acids Research.

The authors kindly made their paper available at their website prior to publication, and our previous discussion on the novel aspects of their approach already covered what is in the paper. On another reading, we found many other papers cited by them as interesting as well. Especially, we like to carefully read the following two papers, when we find time.

1. Fritz MH-Y, Leinonen R, Cochrane G, Birney E. (2011) Efficient storage of high throughput DNA sequencing data using reference-based compression. Genome Res.;21:734-740.

2. Liu Y, Schmidt B, Maskell DL Parallelized short read assembly of large genomes using de Bruijn graphs. BMC Bioinformatics 2011;12:354.

Our NGS reference list is updated with link to Quip paper.


Written by M. //

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