README_read_clean

The script 3_tag_primer_clipping_clean_derep_pbs.sh is based on the pipeline available in the following address:
https://github.com/frederic-mahe/swarm/wiki/Fred's-metabarcoding-pipeline
The script does the whole step at once:

1. Remove tags and primers from demultiplexed sample files
2. Processes a series of format and cleaning steps
3. Convert the clean and trimmed fastq to fasta, adding error rate and size to the header
4. Run the dereplicaion by sample files
5. creates the quality file with the amplicon id, error rate and abundance, necessary for clustering.

Attention! The cutadapt default behaviour is to trim out the adapters after demultiplexing, but I left the action=lowercase argument in order to allow the adapters/tags/primers 
visual inspection.