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[REVIEW]: pycoQC, interactive quality control for Oxford Nanopore Sequencing #1236
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@george-githinji, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
Review checklist for @george-githinji
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referenced this issue
Feb 5, 2019
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To fix this do the following two things:
For a list of things I can do to help you, just type:
Dear @a-slide, we are starting review in this issue tracker. To expedite the review process do you mind going through above list of check boxes and make sure they can be ticked (you can't tick them). Also check the PDF output carefully. Ping us here when you are done.
I confirm that I can tick all the boxes, except automated tests. Indeed, there is no straightforward way to do it as the outputs of pycoQC methods are dynamic plots. One possibility is to inspect visually the outputs and compare it with other software which I have done. Reports generated from the same datasets with pycoQC, Nanoplot and MinIONQC are available online at https://www.ebi.ac.uk/~aleg/data/pycoQC_test/comparison/. Although the 3 programs have different implementation, the results are similar for all 3 summary files tested. If this is an acceptable solution to you, I am happy to upload the datasets on Zenodo to get a DOI.
In addition, I made a dew minor changes in pycoQC and updated the software version to 2.2.1.