I have some fastq files with sequences which I reconstructed by merging forward and reverse reads using bbmerge. The 5' and 3' end of said reads must contain a 6bp inline barcode for contamination control.

I'm looking for a package to extract the 6bp at the beginning and end of the sequence, match them to my database of barcodes while allowing for a set number of nucleotide mismatched (in case of amplification errors), and report:

1. If no recognizable barcodes are present in sequence.
2. If barcodes are present and match. If there are mutations in the barcodes, the script must report the number of mismatches.
3. If barcodes are present but do not match. Again, if there are mutations in the barcode, the script must report the number of mismatches.
4. The size of the insert if barcodes are present.

I can write a bio python script to perform this procedure, but before reinventing the wheel I'd like to know if there a packages that already implemented and standardized the analyses of inline barcodes and perform the tasks described above.