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Multiple sequence alignment

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Ryan Wick edited this page May 15, 2020 · 21 revisions

Requirements

Concept

Running Trycycler msa

Settings

Output

Toggle table of contents Pages 26

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

Home
Software requirements
Installation
How to run Trycycler
- Quick start
- Step 1: Generating assemblies
- Step 2: Clustering contigs
- Step 3: Reconciling contigs
- Step 4: Multiple sequence alignment
- Step 5: Partitioning reads
- Step 6: Generating a consensus
- Step 7: Polishing after Trycycler
Illustrated pipeline overview
Demo datasets
Implementation details
FAQ and miscellaneous tips
Other pages
- Guide to bacterial genome assembly (choose your own adventure)
- Accuracy vs depth

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