Supernova 10X Genomics - estimation of gap length

Question

[MH85]

Hi everyone,

Could somebody explain to me, how the Supernova assembler (10X Genomics) estimates the length of gaps during genome assembly, please?

I am sorry, I did not get it from the 10X Genomics web page (https://support.10xgenomics.com/de-novo-assembly/software/pipelines/latest/output/generating) neither from Weisenfeld et al. 2017 Genome Research 27:1–11.

Thanks a lot in advance Milos

[MH85]

I got the answer from 10x Genomics Support. BTW, they were very quick, kind, and helpful. Well, if somebody needs the answer in the future, here is the one from the 10X Genomics:

" Gaps captured by read pairs are 100Ns.Cycles are broken and prefixed with 10Ns the larger gaps are estimated using the barcodes as described in the supplementary file https://www.biorxiv.org/content/early/2016/08/19/070425.