Workflow script

The main difference is the addition of a script that runs all steps from dada2filter.R to dada2bimers.R.

Smaller changes:

• Check that the user doesn't call for error model estimation from more samples than exists. If so, set to all samples.

• Set default for the parent overabundance parameter (--overab) to 2, the default for the DADA2 function.

Fixed sequence names

Sequence naming was broken in dada2idseq.R 0.1, fixed in v. 0.2.1 of the script.

Build sequence table

This release is identical to v0.9.0 (except for some minor things) except for the addition of dada2idseq.R, a script that builds a sequence table with names instead of sequences plus outputs a fasta file that can be used by dada2taxonomy.R.

First release

All scripts except dada2taxonomy.R have been in production, dada2taxonomy.R is new.