Open-reference clustering for all clustering algorithm about deltamp HOT 4 CLOSED

In GitLab by @lentendu on Sep 19, 2018, 17:45

This is not possible with swarm

from deltamp.

In GitLab by @lentendu on Sep 19, 2018, 17:45

removed milestone

from deltamp.

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.

from deltamp.

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

from deltamp.