Data volumes generated by next-generation sequencing (NGS) technologies is now a major concern for both data storage and transmission. This triggered the need for more efficient methods than general purpose compression tools, such as the widely used gzip method.
Researchers at INRIA/IRISA/GenScale have devloped a novel reference-free method meant to compress data issued from high throughput sequencing technologies. Their approach, implemented in the software LEON, employs techniques derived from existing assembly principles. The method is based on a reference probabilistic de Bruijn Graph, built de novo from the set of reads and stored in a Bloom filter. Each read is encoded as a path in this graph, by memorizing an anchoring kmer and a list of bifurcations. The same probabilistic de Bruijn Graph is used to perform a lossy transformation of the quality scores, which allows to obtain higher compression rates without losing pertinent information for downstream analyses.
Schematic description of LEON’s path encoding. In the upper part, the mapping of two reads to the de Bruijn Graph is represented. Kmer anchors are shown in blue, bifurcations to (read on the left side) or difference from the graph (read on the right side) are respectively highlighted in green and red. In the bottom part, the corresponding path encodings for these two reads are shown: the index of the kmer anchor, and for each side the path length and bifurcation list
LEON was run on various real sequencing datasets (whole genome, exome, RNA-seq or metagenomics). In all cases, LEON showed higher overall compression ratios than state-of-the-art compression software. On a C. elegans whole genome sequencing dataset, LEON divided the original file size by more than 20.
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Last Wednesday, 10/31/2018, we were made aware that Fuel Rewards members were affected by a technical issue related to Hog Wild Wednesday. Affected members did not receive their additional 5 cent per gallon discount. Our team is working to identify the members affected and add an additional 5 cents per gallon savings into each of those accounts. If you visited a Road Runner Shell location last Wednesday and did not receive your additional 5 cent per gallon savings, you will receive an email letting you know when that has been applied to your account. We greatly appreciate each of our customers and their loyalty to the Road Runner brand. With that, we want to ensure you that this technical issue has been addressed and will not happen again. We look forward to seeing you all Wednesday for Hog Wild Wednesday- where Gold Members save at least 10 cents per gallon! And as always, WPS! See full post on Facebook.com[…]
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