Sequence length statistics

[Nicholas_Bokulich]

@Joanna

I wonder if these sequences should be taken care of e.g. by removing them. Is this a common thing to do QIIME2?

Hi @Joanna, it depends on the target gene and primer set used, but I am not sure I'd describe this as a common scenario. It is certainly possible to filter sequences by length, though! See here:

Filtering out ASVs from DADA2 based on length

Just wanted to toss out one more option for length-based filtering: qiime feature-table filter-seqs \ --i-data seqs.qza \ --m-metadata-file seqs.qza \ --p-where 'length(sequence) > 4' \ --o-filtered-data filtered-seqs.qza This works by viewing the FeatureData[Sequence] as Metadata, and then using a SQL-where clause to compute the length. The advantage here is then you don't have to export anything. This command above would keep any sequences longer than 4 nts.