Comments (9)
Relevant pre-print https://www.biorxiv.org/content/10.1101/2022.01.31.478527v1
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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.
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If we're closing this issue, can we open two new ones to remember @gregmedlock 's points above #22 (comment)
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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
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I was thinking more of investigating MEGAN at this point, I will update the description of the issue.
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There doesn't seem to be any further updates from metaMaps so going to close this (sadly)
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@sofstam could you do that?
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Removing this from the first release milestone as the only current candidate, metaMaps is stuck due to an upstream bug (see)
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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
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Related Issues (20)
- Decontamination: add hostile for host removal HOT 5
- https://github.com/nf-core/taxprofiler/pull/318
- Enhance Profiler ganon by adding combineProfilesWithDatabase
- Profiling: consider cross-database merge for KMCP
- KMCP profile mode forced for all databases
- Add Eukdetect
- Add small files to tower.yml
- Simplify test profiles in CI test HOT 1
- Update KrakenUniq to 1.0.4 due to bug causing misreading if input files
- Update to nf-core tempate 2.10
- Add support for sequencing coverage esimates with nonpareil HOT 4
- process `MEGAN_RMA2INFO` JavaFX detected no fonts error HOT 1
- Taxpasta parameters produce an error exit status of 2 which asks for a taxonomy even though kraken2 and centrifuge have worked. HOT 1
- Taxpasta parameters produce an error exit status of 2 which asks for a taxonomy even though kraken2 and centrifuge have worked. HOT 1
- process `VISUALIZATION_KRONA` mis-combined channel by wrong index HOT 3
- `KRONA_KTIMPORTTEXT` input file name collision if same 'db_name' is assigned to kraken2 and bracken HOT 5
- MetaPhlAn4 full index provide duplicated 'NCBI_tax_id' to taxpasta as input HOT 1
- Allow hibf in ganon? HOT 8
- General version update of all tools
- megan version 6.21.7 throw `java.lang.NullPointerException` error HOT 5
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