GW_to_phylogeny : Create nucleotide sequences in which bases of SNPs of each strain are collected for use in phylogenetic analysis.

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Acceptable input formats:

• Per-base information on coverage exported as tsv format on CLC Genomics Workbench.
• Annotation and variant information exported as csv format on CLC Genomics Workbench.

Required libraries and programs:

• Perl5 (Tested on 5.22.1)
• SQLite3
• Perl module DBI
• Perl module DBD::SQLite
• Perl module Term::ReadKey
• Perl module Text::CSV_XS

Usage:

   depth2db.pl --db-file filename.db [--yes] strain1=strain1.tsv [strain2=strain2.tsv ..]

Options:
   --db-file : SQLite db file

   --yes : do not prompt before overwriting

   make-snpseqs.pl --db-file filename.db --strains strain1[,strain2[, ...]] \
   --type {strict|allow-gaps|reference} [--min-coverage N] [--max-coverage N] \
   --snp-pos-file filename.csv --out filename.fasta --summary filename.txt  

Options:
   --db-file : SQLite db file

   --strains : comma separated strain list to process

   --type : processing method for SNPs without relevant depth
   
   --min-coverage : minimum coverage
   
   --max-coverage : maximum coverage
   
   --snp-pos-file : annotation and variant csv file
   
   --out : output fasta file

   --summary : processing report