### PIPELINE FOR DEMULTIPLEXING NANOPORE READS WITH ILLUMINA LIBRARIES ###

### CREATED BY CLAUDIA SANCHIS LOPEZ 2023 ###

##PIPELINE##
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# 1. Get the whole index (uniq and common sequences) of illumina in nanopore reads (using blastn)
# 2. Get uniq index, the indentifier of each index and its coordinates 
# 3. Calculating text similarity distance of each uniq index, and generate output matrix of each adaper
# 4. Extract the best match index according to the text similarity
# 5. Asign a sample if the best match index make sense with the real combination of indexes used in the wet lab (samples_index_captura_mcps082023 file)
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#FILES:
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#./trimmed_reads.00.fasta: the input fasta file are the trimmed reads of nanopore
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#./out_dir/ shows all the intermediate files created for one fraction (00) of the total analysis as example of the outputs
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#./demultiplex.sh: the pipeline calling all the python scripts in this folder.
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#./samples_index_captura_mcps082023: the experimental design of the indexes for each sample