Starting to Understand the SPAdes Papers

Starting to Understand the SPAdes Papers

Last week, we posted an interesting abstract titled “From de Bruijn Graphs to Rectangle Graphs for Genome Assembly”. Thanks to Aaron Hardin and Nikolay Vyahhi, we received two fascinating papers to read over the weekend.

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

[From de Bruijn Graphs to Rectangle Graphs for Genome Assembly by Nikolay Vyahhi, Alex Pyshkin, Son Pham and Pavel A. Pevzner

Their primary objective was to use complete information from paired end (or mate pair) reads to assemble genomes. Paired end reads are usually treated by typical de Bruijn assemblers as two separate reads. This morning, we joked about smashing LEGO pieces, and you can see that treating two reads from paired end sequencing as unconnected entities is conceptually equivalent to smashing LEGOs by hammer (not Hammer). The process leads to loss of valuable information. For example, when each read is 100 nt long, using paired end in the first round of assembly can make read length go up to 200 or 225 nt. There is world of difference between a genome covered 50x with 225 nt reads, and genome covered 100x with 100 nt reads. The difference is even more important in single cell sequencing or transcriptomics, where the depth of sequencing varies widely between regions. SPAdes paper was motivated by single cell sequencing.

Paired end information is ignored, because pairing is difficult to handle under de Bruijn graph formalism due to variable distance between the paired reads. SPAdes paper deals with that challenge by conceptually treating the variable distances as error, and adjusting errors as an ‘error correction step’, just like most de Bruijn graph-based assembly algorithms run an error- correction on nucleotides.

SPAdes papers have many innovative ideas, but here are two we have been able to digest so far -

(i) Building de Bruijn graph with variable k-mer sizes: We discussed earlier that using small k-mers can create dubious paths through de Bruijn graphs, whereas long k-mers can get the graph fragmented. One common strategy is to use Velvet with variable k-mer sizes and somehow merge the assemblies, or pick the one with best N50. Instead SPAdes incorporates variable k-mer size in the de Bruijn graph itself.

(ii) k-bimer adjustment and paired assembly graph: These algorithms are essentially the core of the paper, and are developed to properly consider paired end reads. We cannot explain it all today, but we will try to briefly explain where the rectangles come from. Regular de bruijn graphs for k-mers can be conceptually seen to form lines or one-dimensional structures, especially in the regions of the graph without repeats. The rectangles of SPAdes papers are formed from pairs of such linear simple regions (mathematically described as h-edge in the paper). Since the lengths of various non-repetitive regions are different, you get rectangles with two sides of unequal lengths. The second paper by Nikolay Vyahhi takes that rectangular graph as a mathematical abstraction, and presents a solution.

We will add more on the above point with few nice pictures, when time permits.

Written by M. //