MiSeq post run washes: beware of expired sodium hypochlorite

Bleach, or sodium hypochlorite (NaOCl) is optionally used during MiSeq post-run washes in order to eliminate run-to-run carryover of library template. I noticed a cloudiness in our 5% sodium hypochlorite. This stock solution was purchased several years ago and stored in the fridge as indicated on the label. The bottle had no expiration date. After some online searching it became obvious that bleach has a (very) limited shelf life, depending on the temperature and concentration. After several years our stock had decomposed to saltwater, and seemed to have some fungal growth! Fortunately our MiSeq seemed unaffected; a cursory check found no indications of  run cross-contamination, and a later instrument annual maintenance found the capillaries clear and clean. Nevertheless, the moral of the story is: regularly buy fresh NaOCl for your post-run washes! 

Guppy update - "super-accurate" model

Towards the end of May Oxford Nanopore released a new version of the Guppy basecaller. This version includes the Bonito basecaller model, which I previously tested and found that the quality scoring was broken. You can now select among 3 models; fast, HAC, and sup, with sup ("super accurate") the slowest but most accurate. I put our five genomic test datasets through the new version, using the sup model. I am pleased to see that the quality scoring problem from Bonito has been fixed. The sup model shows a small increase in the raw accuracy. This comes at the cost of slower basecalling speeds. In conclusion, another nice upgrade in accuracy. One of these days I must do some assembly benchmarks* to see if this translates into better assemblies! Previous testing by a colleague of mine indicated that this was not always the case. 

* I just need to learn how to do assemblies :-)

Error rates were calculated using Heng Li's one liner. No quality trimming was applied, except for Species 5 which had a minimum quality score of 7. 

The read quality estimates are now at least somewhat correlated to how similar the sequences are to the reference.