Nanopore reads are classified with a set of taxonomic profilers

[sofstam]

Classifiers that can be tested or investigated for nanopore reads:

• MetaMaps
• MEGAN-LR, further investigation is needed if this tool can be used in the pipeline
• Kraken2
• Centrifuge
  • centrifuge/centrifuge module needs to be added to taxprofiler
  • centrfuge/kreport module needs to be added to taxprofiler
• Kaiju
  • kaiju/kaiju module needs to be added to taxprofiler
  • kaiju/kaiju2table module needs to be added to taxprofiler

[Midnighter]

Relevant pre-print https://www.biorxiv.org/content/10.1101/2022.01.31.478527v1

[jfy133]

Note that MEGAN itself is a GUI based tool, and may not be 💯 suitable for pipelining (however sometimes some of the functionality is present in utility tools packged with MEGAN, so it may still be possible - I actually plan to include the MEGAN container anyway, as it has a useful tool to convert MALT RMA6 files into tables) - so it's something worth investigating

[sofstam]

I was thinking more of investigating MEGAN at this point, I will update the description of the issue.

[gregmedlock]

FYI the preprint that @Midnighter linked used PacBio's snakemake workflow for HiFi/nanopore reads with MEGAN-LR, and describes which executable tools + files are used from the MEGAN community edition, so it should be possible : )

Also, this may be out-of-scope until after a stable release, but a bespoke implementation of BugSeq-V2 seems worth investigating given its performance in that preprint.

[jfy133]

Removing this from the first release milestone as the only current candidate, metaMaps is stuck due to an upstream bug (see)

[jfy133]

There doesn't seem to be any further updates from metaMaps so going to close this (sadly)

[Midnighter]

If we're closing this issue, can we open two new ones to remember @gregmedlock 's points above #22 (comment)

[jfy133]

@sofstam could you do that?

[jfy133]

note that when I look at the MEGNA-LR related snakemake pipeline, that's just actually minimap2 + a LCA... we could do that instead I guess but it's a whole extra (rather large workflow). Although admittedly with tools we already have in taxprofiler