(be sure to update your PERL5LIB appropriately):

• Carp
  
• FileHandle
  
• Getopt::Long
  
• LWP::UserAgent
  
• Pod::Usage
  

• biopython : https://github.com/biopython/biopython
• seaborn : https://seaborn.pydata.org/

Be sure to add these programs to your PATH

• MAFFT : https://mafft.cbrc.jp/alignment/software/ (no extensions are necessary)
• CONSENT-correct : https://github.com/morispi/CONSENT/releases/tag/v2.2.2
• PRANK : http://wasabiapp.org/software/prank/
• PROBCONS : http://probcons.stanford.edu/
• Muscle : https://github.com/rcedgar/muscle/
• Hmmer : http://hmmer.org/
• BLAST : https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
• CD-Hit : https://github.com/weizhongli/cdhit
• VSearch : https://github.com/torognes/vsearch
• QIIME2 : https://qiime2.org/

There is a multi-stage processing approach that takes raw RoC-ITS reads and ultimately generates clusters of distinct 16S-ITS operons associated with a particular genera:

1. Run the python pipeline to generate RoC-ITS sequences from the raw Nanopore RoC-ITS reads
2. Run the perl pipeline to organize RoC-ITS sequences roughly into genera
3. Run the perl pipeline to further cluster individual genera groupings into distinct RoC-ITS operons