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How variants are chosen for the consensus sequence
Ryan Wick edited this page Jan 5, 2021
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This page goes into more detail on how Trycycler produces a consensus sequence. Specifically, when faced with multiple different variants of a sequence, how does it choose which one is best?
Take this hypothetical MSA as an input to Trycycler consensus:
GGAGGAGCTTTT-CGCCGCAGTCAACGAA-TAGCGTCTGAAAACGTGTATCATATCTTGCCTCGAAAAGCCGCACT
GGAGGAGCTTTTTCGCCGCAGTCAAC--A-TAGCGTCTGAAAACGTGTATCATCTCTTGCCTCGAAAATCCTCACT
GGAGGAGCTTTTTCGCCGCAGTCAAC--ATTAGCGTCTGAAAACGTGTATCATGTCTTGCCTCGAAAATCCTCACT
GGAGGAGCTTTTTCGCCGCAGTCAAC--A-TAGCGTCTGAAAACGTGTATCATCTCTTGCCTCGAAAAGCCGCACT
GGAGGAGCTTTT-CGCCGCAGTCAAC--A-TAGCGTCTGAAAACGTGTATCATGTCTTGCCTCGAAAATCCGCACT
Trycycler first divides the MSA into 'same' and 'different' chunks:
GGAGGAGCTTTT - CGCCGCAGTCAAC GAA- TAGCGTCTGAAAACGTGTATCAT A TCTTGCCTCGAAAA GCCG CACT
GGAGGAGCTTTT T CGCCGCAGTCAAC --A- TAGCGTCTGAAAACGTGTATCAT C TCTTGCCTCGAAAA TCCT CACT
GGAGGAGCTTTT T CGCCGCAGTCAAC --AT TAGCGTCTGAAAACGTGTATCAT G TCTTGCCTCGAAAA TCCT CACT
GGAGGAGCTTTT T CGCCGCAGTCAAC --A- TAGCGTCTGAAAACGTGTATCAT C TCTTGCCTCGAAAA GCCG CACT
GGAGGAGCTTTT - CGCCGCAGTCAAC --A- TAGCGTCTGAAAACGTGTATCAT G TCTTGCCTCGAAAA TCCG CACT
- Home
- Software requirements
- Installation
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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