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Add automated blastx-like LCA of post-spades contigs to demux_plus.wdl #784

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dpark01 opened this issue Feb 6, 2018 · 1 comment
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@dpark01
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dpark01 commented Feb 6, 2018

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.

@dpark01 dpark01 added this to To Do (this release) in v1.19.3 via automation Feb 6, 2018
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tomkinsc commented Feb 6, 2018

Related to this, a ghostx package has been added to bioconda so we can more easily include/evaluate it, as well as one for ghostz.

@dpark01 dpark01 moved this from To Do (this release) to Backlog (not necessarily this release) in v1.19.3 Mar 26, 2018
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