Comments (1)
Traces don't provide haplotyping information and therefore, tracy indeed first threads the reference through the peaks and whatever is left constitutes the second allele. You can also compare traces directly without a reference, e.g., a wildtype trace against a mutated trace. Pearl (the assemble subcommand) is essentially a multiple trace alignment, either against a reference (reference-guided assembly) or de novo. It's useful to find "common" alleles that are in many traces but not in the reference.
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Related Issues (20)
- SCF version greater 2.9 required! HOT 4
- Only single-chromosome FASTA files are supported HOT 1
- Can tracy assemble trim option be disabled? HOT 1
- Decompose doesn't give bcf file give json instead HOT 3
- Base quality and consensus generation HOT 7
- How can I provide a file with a list of input files to tracy? HOT 2
- Indigo HOT 4
- Cannot execute Tracy binary on mac HOT 5
- Bioconda tracy package runs very slowly where precompiled binary is fast HOT 2
- terminate called while attempting to run tracy on WSL HOT 1
- [feature request] Further options to control trimming with consensus HOT 5
- -p signal to noise ratio HOT 1
- Annotation error in the results generated sanger sequencer HOT 4
- `Couldn't anchor the Sanger trace in the selected reference genome.` error in tracy but not in Indigo HOT 3
- Issues Installing/Compiling on Mac HOT 2
- docker images differences between quay.io and dockerhub HOT 4
- Options for specifying overlap, 'fracmatch' in consensus subcommand
- Can tracy's consensus option be updated?
- Hemizygous calls HOT 2
- basecall problem HOT 2
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