Page Index - mossmatters/HybPiper GitHub Wiki

28 page(s) in this GitHub Wiki:

• Home
• Links to other wiki pages:
• Overview
• 1.0 Preparing your files
• 1.1 Read files
• 1.2 Target file
• 2.0 Running the pipeline
• 2.1 Command overview table
• 2.2 Command overview descriptions
• 2.2.1 Main sequence assembly and extraction pipeline
• hybpiper assemble
• 2.2.2 Post assembly and extraction pipeline
• hybpiper stats
• hybpiper recovery_heatmap
• hybpiper retrieve_sequences
• hybpiper filter_by_length
• hybpiper paralog_retriever
• 3.0 Summary
• Detecting putative chimeric loci sequences
• Full pipeline parameters
• HPC
• HybPiper Legacy Wiki
• Installation
• Introns
• Paralogs
• Results and output files
• Troubleshooting, common issues, and recommendations
• Tutorial