This is a question from the Oxford Nanopore community, from user Michael Radzieta:
I have sequenced some plasmids using the rapid barcoding kit, I have attempted to assemble the data using several programs (unicycler, spades, ra) but nothing has been able to assemble the plasmids I am expecting. I have read that if the coverage is too high, then it can negatively affect the assembly. Based on the approximate size of my plasmids and the number of filtered reads I have, the coverage is estimated at >5000.
Can anyone recommend a tool to subsample or normalise nanopore reads to a certain depth, such as 100x coverage?