[ymc]

Oh well, I figured it out.

I used ERX593921 data to polish the sample data which is from ERX708228 to ERX708231. After I used the fast5 from the correct archive, I was able to complete the run: (REF=polished, QRY=K12_MG1655)

[REF] [QRY]
[Sequences]
TotalSeqs 1 1
AlignedSeqs 1(100.00%) 1(100.00%)
UnalignedSeqs 0(0.00%) 0(0.00%)

[Bases]
TotalBases 4614015 4641652
AlignedBases 4612566(99.97%) 4620207(99.54%)
UnalignedBases 1449(0.03%) 21445(0.46%)

[Alignments]
1-to-1 86 86
TotalLength 4613201 4627972
AvgLength 53641.87 53813.63
AvgIdentity 99.23 99.23

I think better error messages in this case will be welcomed.

[ymc]

The ERX708228-31 data seems to have much higher yield for 2D reads than ERX593921. Why is that? Don't they all have the same R7.3 Chemistry? Or some sort of filter was applied for ERX708228-31? If so, what was that filter?

Archive #read length #2Dread length 2Dyield
593921 70531 311.56M 11823 64.53M 20.71%
708228 25353 150.33M 8451 52.26M 34.76%
708229 16917 61.57M 5639 21.91M 35.58%
708230 8565 46.05M 2855 16M 34.74%
708231 15975 123.29M 5325 43.44M 35.24%

[ymc]

I read the two papers more carefully and noted the versions of Chemistry, Sequencing Kit and Metrichor for each run:

ERX593921 is (R7.3, SQK-MAP-003, Metrichor 1.2.2 r1.5)
ERX708228 is (R7.3, SQK-MAP-003, Metrichor 1.9)
ERX708229-31 is (R7.3, SQK-MAP-003, Metrichor 1.9)

So the difference was due to using older version of Metrichor for ERX593921?

Does each run correspond to one ONT box? If that's the case we are only getting 133.6Mb for $4,000? Then ONT is not competitive at all in bacterial de novo assembly, right?