Comments (2)
d4straub
commented on September 23, 2024
All taxonomic classification subworkflows (see here) use ASV sequence tables (fasta) after the various filtering steps (see e.g. DADA2). In any case, a subworkflow such as here would be great.
I propose to use LCA after blastn (or as Daniel Lundin proposed rather vsearch) in a separate taxonomy assignment subworkflow. The output of that subworkflow would be the downstream-compatible taxonomic classification.
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a4000
commented on September 23, 2024
A subworkflow sounds like a good idea, thanks
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Related Issues (20)
- ERROR ~ Error executing process > 'NFCORE_AMPLISEQ:AMPLISEQ:DADA2_MERGE .........has been broken HOT 3
- ANCOM-BC for differentially abundant taxa HOT 2
- ERROR: R_HOME ('/usr/local/lib/R') not found HOT 5
- Misleading error message when samples are not passing filterandtrim HOT 1
- Accessing 16S gene identifiers HOT 13
- DADA2 split regions singularity HOT 13
- multi-region analysis: sidle/reconstructed/reconstructed_merged.tsv OCCATIONALLY mis-formatted HOT 1
- Running test error HOT 1
- Abundance plots for qiime2 results without metadata provided HOT 3
- Adding ONT read support for ampliseq HOT 2
- `overall_summary.tsv` sometimes with misleading numbers in 2.9.0 HOT 11
- Analyse data set that contains unknown primer set HOT 5
- Cutadapt with "-u" instead of "fw/rv_primer seq" HOT 1
- There is no qiime2 result file in the results HOT 2
- Misleading text in output documentation HOT 1
- Add MACSE to enable frame-shift detection for COI HOT 6
- Pipeline fails when run with a lot of cores HOT 6
- Error "Can't stage file https://files.plutof.ut.ee:" Download fail HOT 7
- Taxonomy database choices not validated against permitted values since 2.9.0 HOT 3
- New (10.0) version of Unite databases available to `--dada_ref_taxonomy`
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