Description
Hello,
I've got a question regarding the argument --maxaccepts of the vsearch command --cluster_fast:
The manpage states the following about maxaccepts:
"The search process sorts target sequences
by decreasing number of k-mers they have in common with the query sequence, using
that information as a proxy for sequence similarity. After pairwise alignments, if the
first target sequence passes the acceptation criteria, it is accepted as best hit and the
search process stops for that query. If --maxaccepts is set to a higher value, more hits
are accepted"
What is exactly meant with "If --maxaccepts is set to a higher value, more hits
are accepted" ?
What will happen when another hit is accepted?
I guess the target sequences are the centroids or seed sequences of the clusters in this case?
So these are clusters (i.e. target sequences) are sorted based on number of k-mers in common, which will likely resemble pairwise sequence similarity.
I can understand that if --maxaccepts 1(default) is specified, vsearch then starts to go through these pairwise alignment and selects the first one that matches the criteria (e.g. 97% similarity). Then the query sequence is placed in that cluster(?)
But if e.g. --maxaccepts 2 is specified, the query sequence can be accepted in two clusters? Or how does this work?
I can imagine that the first alignment that matches the criterion is not the best one and so that you preferably check multiple accepted target sequences and select the best one from that (i.e. place your query sequence in the cluster that matches best). Is that what --maxaccepts is about? In that case, I would except a description like: " If --maxaccepts is set to a higher value, more hits are accepted and the best matching target sequence is finally selected as hit" or something like that.