nanopore tools - Githubissues

bgruening / galaxytools

:microscope::books: Galaxy Tool wrappers

MIT License

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nanopore tools #777

Open bgruening opened 6 years ago

bgruening commented 6 years ago

Tools on which we are working currently:

Tools that are already integrated:

nanopolish
racon
canu
wtdbg

ping @willemdek11, @shiltemann, @mmiladi

shiltemann commented 6 years ago

Great! Some more from our side:

[x] poretools
[x] plasflow
[x] bandage
[x] porechop
[x] filtlong

mmiladi commented 5 years ago

Wonderful Saskia. Updates:

[x] Flye
[x] Graphmap

mmiladi commented 5 years ago

Hi @shiltemann, It seems all these tools are integrated now. Very nice!

Regarding assembly graph visualization and supporting format, bandage looks promising. Flye also outputs the gfa format and the connectivity graph in GraphViz graph_dot format. Bjoern defined the format here: https://github.com/galaxyproject/galaxy/pull/6760

If it make sense, we can introduce gfa, spades and other formats as well. Which of them is supported by Bandage?

shiltemann commented 5 years ago

I think that would make a lot of sense :+1:

Bandage supports formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA :)