for visualizing alpha diversity.
shows that one in five taxonomy annotations in SILVA and Greengenes are wrong.
shows that taxonomy prediction accuracy is <50% for V4 sequences.
shows low accuracy of closed- and open-ref. QIIME OTUs.
shows 97% threshold is wrong, OTUs should be 99% full-length 16S, 100% for V4.
UPARSE tutorial video
posted on YouTube. Make OTUs from MiSeq reads.
New in v11
OTU errors and biases
Commands to convert file formats
FASTQ file format options
Phred (Quality) scores in FASTQ files
Calculating average Phred (Q) scores is a bad idea
Annotations in sequence labels
Sequence database files
IUPAC codes for sequence wildcard letters N, X etc.
Why doesn't USEARCH support gzipped FASTQ files?
CIGAR strings in SAM files
USEARCH Database (UDB) files
Mothur file formats
QIIME file formats
OTU table file formats
NAST multiple alignment files (nastout)
Newick tree format