Open ImagoXV opened 8 months ago
vsearch log
Reading file /tmp/.tmp_NanoASV/FILTERED_barcode20.fastq.gz 100%
181569135 nt in 115928 seqs, min 1300, max 1700, avg 1566
Masking 100%
Sorting by abundance 100%
Counting k-mers 100%
Detecting chimeras 100%
Found 0 (0.0%) chimeras, 115928 (100.0%) non-chimeras,
and 0 (0.0%) borderline sequences in 115928 unique sequences.
Taking abundance information into account, this corresponds to
0 (0.0%) chimeras, 115928 (100.0%) non-chimeras,
and 0 (0.0%) borderline sequences in 115928 total sequences.
If clustering, then it's not ASV treatment anymore.
You are right. Dereplication of identical sequences is easy, whereas approximate dereplication is hard. That's an issue with NanoPore sequencing: reads need to be dereplicated for the de novo chimera detection, but dereplication requires a certain level of grouping (ASV, or OTU, or taxo-grouping).
Yep, so I guess the chimara detection step is totally useless in that context.
I guess we might detect chimera after alignment ? Allowing to have a common base for "dereplication" like information.
I don't know.
We need to look at the new chimera detection algorithm in vsearch. It should now work for sequences with errors. Although, I think it still requires for sequences to have abundance values, so a form of clustering before chimera detection.
Vsearch seems to never detect chimera with default parameters.
I think it lies on the fact that sequences are not dereplicated and therefore do not have a "count" section in fasta header. However, I think dereplication might not work because vsearch expects 100% similarity. Which is rarely (if not) achieved with nanopore amplicon sequencing. Efficient dereplication would come from accepting a certain variability threshold that would end up being clustering. Such clustering with vsearch performs well with a --id 0.7. Which is significantly lower than what we would want to accept for dereplication. If clustering, then it's not ASV treatment anymore.
I need to discuss it with you @frederic-mahe