Open dhoogest opened 3 years ago
We'll need to bump this in response to https://gitlab.labmed.uw.edu/molmicro/NGS16S/-/issues/285
I've got changes in #49 to complete this issue. Need to find a sample which demonstrates significant abundance of chimera and add that to the ngs16s test data set. /cc @nhoffman
@dhoogest You asked for test specimens, here's one from today where 10% reads were dropped at the chimeras removed filtering step https://share.labmed.uw.edu/molmicro/markergene/22N0238_NGS16S/report/22R192-11/ Seems as good as any for a validation run, we know our current version of dada2 is flagging svs as chimeric here.
There is a small R script in the current NGS16S pipeline which extracts from the
dada2.rda
file the sequences which were dropped as chimeras and outputs a csv with columnsweight
andsequence
. This file is not used for any downstream classification pipeline dependencies, however is useful to have for troubleshooting when a larger fraction of reads is lost during the chimera removal phase. The script currently outputs a file for each sample in the run, but it is not necessary to separate per sample if that is less convenient for the nextflow pipeline