Closed apredeus closed 3 years ago
This is a good start, but Nanopore-Sep2020.conf
should give better results than Nanopore-Jun2020.conf
. Or, if you have a plant genome, try Nanopore-Plants-Apr2021.conf
. And if you have the latest code from GitHub it should also accept --Assembly.consensusCaller Bayesian:guppy5.0.7-a
, which is equivalent to SimpleBayesianConsensusCaller-10.csv
.
If you don't get a satisfactory assembly, please post here AssemblySummary.html
plus the expected genome size and I can help tweak assembly parameters.
Actually turns out I got the best result of all the assemblers I've tried so far, so I'm quite happy with this :) Thank you for the hints, I'll try the newer config file as well.
Hello all,
Just wanted to check if the following command looks reasonable to assemble reads called by Guppy version 5, with "super high accuracy" (Bonito-style models). The 0.7.0 pre-made binary didn't run with
--Assembly.consensusCaller Bayesian:guppy5.0.7-a
throwing an error about unknown caller. I cloned this repo and in the end came up with something like this for the assembly command:Can you comment if this makes sense at all? Read length is limited to 2000 since I have about 50x coverage with median of 13k, so quite a few reads are shorter than the default 10k cutoff.