Page Index - rrwick/Trycycler GitHub Wiki

56 page(s) in this GitHub Wiki:

• Home
• The problem
• The solution
• An important caveat
• Where to begin?
• 2025 update
• Accuracy vs depth
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• Bad dataset analysis
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• Clustering contigs
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• Demo datasets
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• FAQ and miscellaneous tips
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• Generating a consensus
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• Generating assemblies
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• Good dataset analysis
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• Great dataset analysis
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• Guide to bacterial genome assembly
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• How circularisation repair works
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• How multiple sequence alignment partitioning works
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• How read subsampling works
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• How to run Trycycler
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• How variants are chosen for the consensus sequence
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• Illustrated pipeline overview
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• Installation
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• Mediocre dataset analysis
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• Multiple sequence alignment
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• Partitioning reads
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• Polishing after Trycycler
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• Quick start
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• Reconciling contigs
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• Software requirements
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• Starting sequences for circular replicons
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