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Welcome to the CLdb Wiki!

This wiki is a guide to database creation and performing workflows with the database.

Help

• Getting help

For the impatient

• Quick tutorial

Starting out

• Requirements
• Install
• Database setup
• Initial data loading

Workflows

Database management

• Get summary info
• Write tables
• Delete entries
• Check for loci overlap

General data retrieval

• Get a fasta
• GFF3 of loci

Leaders If leader regions not known:

• Find and load leaders If leader regions known:
• Load known leaders

Spacer blast

• blast vs genome
• blast vs nt
• GFF3 of blast hits

PAMs

• get PAMs

Spacer-protospacer mismatches

• protospacer mismatch

Loci presence-absence

• subtype pres-abs ITOL metadata

Plotting loci

• Plotting loci

Classifying subtype of arrays based on direct repeats

• Classify arrays

Target assembly of broken arrays

• Find broken arrays

How do I...?

• HowTo