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Partly motivated by ongoing analyses @tomkinsc is working on, it would be useful to consider a way of automating a way to taxonomically classify the SPAdes-based contigs that are already being produced post-depletion as part of the demux_plus WDL workflow.
Most straightforward way would be running blastx against nr and utilizing some previously-written blast-LCA code from this repository from @yesimon. But we can also explore other blastx-like tools that might have better performance characteristics. DIAMOND is likely to be slower, based on their own documentation (it is intended for a large number of short query sequences, and is often slower than blastx when used on a small number of long query sequences)--but also based on my own experience experimenting with it.
This would formalize and automate a process that Cormac once experimented with.
The text was updated successfully, but these errors were encountered:
Partly motivated by ongoing analyses @tomkinsc is working on, it would be useful to consider a way of automating a way to taxonomically classify the SPAdes-based contigs that are already being produced post-depletion as part of the
demux_plus
WDL workflow.Most straightforward way would be running blastx against
nr
and utilizing some previously-written blast-LCA code from this repository from @yesimon. But we can also explore other blastx-like tools that might have better performance characteristics. DIAMOND is likely to be slower, based on their own documentation (it is intended for a large number of short query sequences, and is often slower than blastx when used on a small number of long query sequences)--but also based on my own experience experimenting with it.This would formalize and automate a process that Cormac once experimented with.
The text was updated successfully, but these errors were encountered: