PacBio CCS reads up to 3 kilobases are now supported. See also PacBioErrfun, the new and recommended error-estimation function for PacBio CCS data. The preprint introducing DADA2’s long-read functionality has information on accuracy and sub-species resolution, and the associated reproducible analyses show PacBio-specific workflows.

The trimRight argument has been added to the filterAndTrim function. This removes the specified number of bases from the end (“right” side) of each read. Default value is trimRight=0 (no such trimming).

primer.fwd has been replaced by orient.fwd in the filterAndTrim function. This option consistently orients mixed-orientation single-end or paired-end reads based on matching the provided sequence fragment to the start or end of each read (or paired read). This features is intended for use with mixed-orientation reads that included sequenced primers. If primers aren’t included in the amplicons, an external re-orientation solution remains preferable.

nbases has replaced the nreads parameter in the learnErrors function. As suggested by the name, this controls the amount of data the machine learning uses by the total number of bases rather than the read count, which is more appropriate given the range of read-lengths in target applications.

collapseNoMismatch now collapses identical sequences as well (previous behavior is togglable).

mergePairs now gracefully handles cases when zero reads succesfully merge.

plotQualityProfile now works correclty when given a directory containing fastq files.