Session 5

Marie-Nelly et al., (2014). High-quality genome (re)assembly using chromosomal contact data

Key findings:

The authors of this article presented a new algorithm to assemble genome sequences. This software, called GRAAL, makes use of the reads obtained by the sequencing platforms and also considers structural information obtained from 3C and Hi-C experimental methods. Such information reflects physical contacts between chromosomal DNA sequences and can be used to generate new genome assemblies or to correct already existing ones. This algorithm showed to be able to reproduce a correct genome assembly for the Saccharomyces cerevisiae reference strain BY4741 using a scrambled set of contigs and a 3C-seq contact map. Such results were robust up to a 100-fold downsampling of the input represented by random subsets of input data. GRAAL also allowed to identify major chromosomal rearrangements produced by two large sequence repeats present in the S. cerevisiae strain YKF1246. Even more, GRAAL was able to detect a more complex genome structure from a Malaysian isolate of S. cerevisiae presenting a set of 8 chromosomal rearrangements verified by PCR and additional re-sequencing. Finally, this method was used to finish and cure the draft genome assembly of the industrially-relevant yeast Trichoderma reesei. Such genome was published as 77 scaffolds that were reduced to 7 large sequences using GRAAL. This result agrees with karyotyping experiments.

Relevance of the article:

This method evaluates the likelihood of different possible assemblies to be consistent with the expected 3C contact map so it is not restricted to produce a single assembly and makes possible to measure the reliability of the proposed assemblies.

GRAAL is useful to resolve repeats and duplications which are the most common issues found in genome assembly projects.

It also showed good results with well-known yeast genomes and with different strains/species showing complex genome structures.

Rating (‘Exceptional – a must read paper’, ‘Very good – worth spending the time’, ‘Good – only if you have time to spare’).

Very good

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