First SQK MAP 006 experiment

We’ve just finally found the time to break open the new SQK-MAP-006 kits from Oxford Nanopore. These kits are notable because they introduce the first really major changes to the chemistry for some time.

The new chemistry is accompanied with a new Metrichor basecaller workflow specific to SQK-MAP-006.

A notable change, looking at the returned FAST5 files, is that the model is now considering signal levels from each of the 4^6 possible combinations of 6-mers when doing basecalling. Before 5-mers were used. Does this mean that the ionic flux through the nanopore is in fact affected by 6 or more bases, rather than the 5 that we initially assumed? Or was 5 simply chosen to simplify the analysis. If the latter - and this seems likely - this may help with basecalling accuracy and it will be interesting to see if it resolves any previously difficult to sequence motifs (we looked at such under represented sequences in our recent paper here in the context of 5-mers:

It does not seem to be supported to call older, pre-SQK-MAP-006 data with the new 6-mer model basecaller.

So far we have done four SQK-MAP-006 runs. Two were generated with natural DNA, and two were generated with the low-input library that includes a PCR step.

Each of the files below are archives of the runs following base calling with Metrichor. We also provide a subset of one of the runs in ‘raw’ format which has the individual signal measurements (i.e. before event detection is carried out).

The raw files are available via the ENA FTP site

Run Basecalled data 2D pass FASTA
MAP-006-1 Basecalled Pass FASTA
MAP-006-2 Basecalled and raw Pass FASTA
MAP-006-PCR-1 Basecalled Pass FASTA
MAP006-PCR-2 Basecalled and raw Pass FASTA

Head over to Jared Simpson’s blog to see some early results of using these data for assembly polishing.


As always, thanks to Josh Quick for his masterful library preparation technique.