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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.



fastx_split command

The fastx_split command divides a FASTA or FASTQ file into roughly equal-sized pieces. The size of a piece is measured by the file size in bytes rather than the number of sequences or number of sequence letters.

The -splits n option specifies the desired number of pieces. You may get n+1 pieces.

The -outname option specifies a pattern for the output file names, which are always FASTA. There must be a '@' character in the pattern, which is replaced by the split number 1, 2, 3...


usearch -fastx_split db.fastq -splits 10 -outname split@.fa