Comments (4)
In GitLab by @lentendu on Sep 19, 2018, 17:45
This is not possible with swarm
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In GitLab by @lentendu on Sep 19, 2018, 17:45
removed milestone
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This would actually be possible with any clustering algorithm, so long all reads used to cluster OTUs in the reference dataset are accessible or could be recreated, the new OTUs could be grafted on it and re-labelled accordingly.
There is of course a possibility that the OTUs slightly differ if both dataset are cluster together due to different unique reads total abundance. This need to be compared for validition.
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The way to go is to compare unique amplicons from current and previous subprojects:
- amplicons of one to multiple OTUs in the current subproject found in a single OTU of the previous subproject are grafted/joined into this former OTU, using the same label
- amplicon from one OTU of the current subproject matching amplicons found in multiple OTUs of the previous subproject are not grafted and kept separated
- labels of new OTU (without any amplicon match) and OTU matching multiple previous OTUs start just after the last OTU of the previous subproject
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Related Issues (20)
- Adapt raw stat R scripts to R 4
- Avoid error if all reads already used in one direction for bidirectionnal libraries
- Allow different set of parameters for checkpointing
- Add header option to mimato
- Add NGmerge as alternative pair-end algorithm
- Allow disabling DADA2 bimera removal HOT 1
- Problem with restart from step when cut_db in the steps
- Problem with cutadapt and anchored adapters
- Feature: similarity based clustering for pair-end sequences which cannot be assembled
- Feature: provide manually curated reference sequences to use for taxonomic identification
- More systematic compression at all levels
- Change minimum number of rank depending on database for cut_db
- Issue with ASV and swarm clustering not accepting N's
- Add version and commit number in env for backward compatibility
- Cluster with multiple previous sub-projects
- Force analyses for unpairable datasets
- Accept gz compress database fasta files
- Set a minimum amount of raw reads found in one orientation to consider this orientation
- Force all samples to belong to the same run for ASV error modl building
- Feature: allow to re-use same optimize quality parameters than a previous subproject
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