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OTU QC: short sequences

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  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.