Hi everyone,
Just a warning that be sure to remove any zero-length sequence from your fastq files before processing them with make.contigs
We recently found out that if somehow there is zero-length fastq sequence in your reads (we used cutadapt to remove nextera adapters, and by default cutadapt will not remove any zero-length sequence). Make.contigs will generate inaccurate number of assembled reads. If you check mothur logs, make.contigs will trigger a lot of warnings, but it keeps on with assembly.
