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11-Aug-2018 New paper describes octave plots for visualizing alpha diversity.

12-Jun-2018 New paper shows that one in five taxonomy annotations in SILVA and Greengenes are wrong.

18-Apr-2018 New paper shows that taxonomy prediction accuracy is <50% for V4 sequences.

05-Oct-2017 PeerJ paper shows low accuracy of closed- and open-ref. QIIME OTUs.

22-Sep-2017 New paper 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.



findorfs command

The fastx_findorfs command finds ORFs in nucleotide sequences in a FASTA or FASTQ file.

The -orfstyle and -mincodons options control ORF identification. The -output option specifies the output filename.

The -ntout output file is a FASTA filename for nucleotide sequences.

The -aaout output file is a FASTA filename for translated (amino acid) sequences.


usearch -fastx_findorfs reads.fastq -ntout -nt.fa -aaout aa.fa -orfstyle 7 -mincodons 16