#### SIGNIFICANT USER-VISIBLE CHANGES

• primer.fwd has been replaced by orient.fwd in the filterAndTrim function.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.

#### BUG FIXES

• 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.

Maintained by Benjamin Callahan (benjamin DOT j DOT callahan AT gmail DOT com)