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rrwick / Unicycler

hybrid assembly pipeline for bacterial genomes
GNU General Public License v3.0
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Unicycler with Ion Torrent #267

Open nclaesnacw opened 3 years ago

nclaesnacw commented 3 years ago

I have some older data from minion and Ion Torrent. The default analysis worked pretty well but spades has an optimised setting --IonTorrent is it possible to run Unicycler with this (some how - not an accepted Unicycler option) or pass in a separate spades assembly to unicycler?

missuse commented 2 years ago

I trust it can be passed via the argument --spades_options

unicycler -s example.fq.gz -o example_uni --spades_options "--iontorrent "

note the extra space at the end "--iontorrent "

EDIT: unfortunately I was not correct, this results in an error after k27 when spades try to restart for the next k-mer length

EDIT2: you can try this: https://github.com/rrwick/Unicycler/issues/175

alexandreflageul commented 1 year ago

Hi all, Hi @rrwick I would like to empahse this issue.
Do you @rrwick recommend to use Unicycler when dealing with Ion Torrent S5 single-ended data ? Your tool will be used in a project between several sequencing platform, and some of them are using IonTorrent S5 technology . Regards Alexandre