Review for "Improved de novo Genome Assembly: Linked-Read Sequencing Combined with Optical Mapping Produce a High Quality Mammalian Genome at Relatively Low Cost"

Completed on 22 Apr 2017 by Keith Robison . Sourced from http://biorxiv.org/content/early/2017/04/19/128348.

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Comments to author

Table 1 -- re-ordering the columns in a logical progression from left-to-right would scan better -- so DISCOVAR, 10X Supernova 1.1, BNG+Supernova 1.0, BNG+Supernova 1.1 (and a bit odd that Supernova 1.0 is omitted)

Table 2 takes a lot of space and isn't really giving more information than Figure 5 -- it would be preferable to have plots like Figure 5 for more chromosomes or a table listing the number of scaffolds & the sizes of scaffolds for each chromosome

The fact that the BNG data greatly reduced the number of scaffolds but had only a modest effect on N50 should be discussed. Is this a limit on scaffolding through centromeres? Do any scaffolds appear to cover an entire chromosome arm? Do any cross a centromere? It might be useful to discuss the known chromosome structure of pinnipeds as described in Beklemisheva 2016 -- adapting their Figure 4 to show how your scaffolds relate to human-seal and dog-seal synteny blocks would be valuable.

Figure 4 -- what region is this? Citation for the fact it is a breakpoint in many genome comparisons? Does this map to a known join vs. human karyotype as described in Beklemisheva? This point would be interesting to see discussed.

p.7 "acrocentric human chromosome which are" -- should identify which acrocentric chromosome(s) are being referred to.

It would be of interest to the genomics community to have a histogram of estimated fragment lengths based on the 10x read clouds and the observed lengths of BNG fragments. It would also be useful to have statistics on anomalously-mapping reads -- those that map outside the scaffold to which the majority of the cloud's reads are assigned. A histogram of number of reads per UMI might also be interesting.

Figure 1 -- move the legend into the plot by labeling the lines-- much easier to read, particularly for the colorblind (red vs. green is never a good choice for that reason)

Discovered a small hitch in one thing I suggested -- the Baikal seal in the Beklemisheva analysis has 2n=32 but Hawaiian monk seals have 2n=34 (Lu et al 2000). According to Arnason 1974 the 2n=34 karyotype is probably ancestral with a single fusion generating the 2n=32 karyotype. Fronicke et al 1997 would make the fused chromosome "S", which is homologous to human chromosomes 17 and 5. Some more musings over on the blog