Help/advice on truncation parameters

[colinbrislawn (Colin J Brislawn)]

Good morning!

@lizgehret

p-trunc-len: Position at which read sequences (forward or reverse) should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles.

Reads that are shorter than this value will be discarded.

There is one exception:

@lizgehret

your sequences will be left untouched if you specify a length in --p-trunc-len that doesn't have any reads greater than the given value.

I'm guessing this is a safety feature from DADA2, which we preserve in the Qiime2 plugin.

Surely, no one wants to remove 100% of their reads!

Perhaps it would be better to throw a warning and reprimand users who discard all their reads with a long trunc-len value. What do you think?