 
 
 Synopsis : nanoasv -d path/to/barcodes -o nanoasv.out [--options]
 
  Option                 Description                                                                     
  --------------------   ------------------------------------------------------------------------------  
   -h ,  --help          Show help message                                                               
   -v ,  --version       Show version information                                                        
   -d ,  --dir           Path to demultiplexed barcodes directory
   -o ,  --out           Path for output directory   
   -db,  --database      Path to reference fasta file                                                          
   -q ,  --quality       Quality threshold for Chopper, default: 8                                       
   -l ,  --minlength     Minimum amplicon length for Chopper, default: 1300                              
   -L ,  --maxlength     Maximum amplicon length for Chopper, default: 1700                              
   -i ,  --id-vsearch    Identity threshold for vsearch unknown sequences clustering step, default: 0.7  
   -ab,  --minab         Minimum unknown cluster total abundance to be kept                        
   -p ,  --num-process   Number of cores for parallelization, default: 1                                 
   --subsampling         Max number of sequences per barcode, default: 50,000                            
   --no-r-cleaning       To keep Eukaryota, Chloroplast, and Mitochondria sequences from phyloseq object
   --metadata            Specify metadata.csv file directory, default is demultiplexed directory (--dir) 
   --notree              To remove phylogeny step and subsequent tree from phyloseq object
   --sam-quality         To tune samtools filtering mapQ threshold, default : 0 
   --requirements        To display personal reference fasta requirements
   --dry-run             Perform a snakemake dry run
   --mock                Run NanoASV with Mock dataset
   --remove-tmp          To remove tmp data after execution. No snakemake resume option if set.

