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Fix missing --out argument in example
Update McCortex citation
Update paths to scripts
Fix anchor/heading ordering
typo save>safe
Add a useful join command example
Updated Join command (markdown)
Added link to McCortex biorxiv paper
Remove incorrect command from link error cleaning section.
Add FAQ on 'git clone --recursive'
Updated VCF Genotyping (markdown)
Rename path -> link
Added notes on using contig confidence in assembly
Add note on removing duplicates
Updated Contributing (markdown)
Added note about git branches
Document --kmer option
Update link cleaning example commands
Added command line examples for link construction
Added link to VCF Genotyping page
Add page on VCF genotyping
Added more details on choosing kmer size
Added simple example and headings
Update join API
Updated Graph Cleaning (markdown)
Add links to papers
Updated Graph Construction (markdown)
Fix command line args in example