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nanopore-wgs-consortium / NA12878

Data and analysis for NA12878 genome on nanopore
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Which is the accuracy of canu.35x.contigs.polished2.fasta? #16

Open fg6 opened 6 years ago

fg6 commented 6 years ago

Hi, first of all: very impressive job, congratulations! My question is if you have tried to estimate also the accuracy of the canu.35x.contigs.polished2.fasta? I guess it must be close to the 99.88% you provide for the 30X accuracy?

By the way, can you confirm which polishing steps were done on both the 30X and 35X assemblies: in the Table 1 it says Pilon 2x, and indeed the contigs are called tigXXXXXXXX_pilon_pilon, but in section "Assembly of the dataset" you say: "We performed a de novo assembly of the 30× dataset with Canu and polished the assembly using both nanopore signal and Illumina data (Table 1). " Did you use also Nanopolish on the 30X/35X assemblies? I guess you only used it for the chr20 assemblies?

Thank you! Fran

skoren commented 6 years ago

Nanopolish was not used on any whole genome datasets, only the smaller chr20 assemblies. The 35x asm is slightly higher but similar to the 30x accuracy (99.31% vs the reference and 99.88% with an independent set of Illumina data).