OTU QC: short sequences
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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.



OTU QC: short sequences

See also
  Quality control for OTU sequences

The PCR reaction used to create a sequencing library can create anomalous short constructs due to e.g. to secondary structure formation. These can easily be recognized by using fastx_info to check the length distribution ("Lengths ... min" gives the shortest and "low" the first quartile), or use sortbylength and look at the sequences towards the end of the output file. Using sortbylength with the minseqlength option removes the short sequences. You could also use the fastq_minmergelen and fastq_maxmergelen options of fastq_mergepairs. You can use PCR amplicon prediction on a reference database for your gene to determine the valid length range for your amplicons.