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.