FlexTyper is a tool which enables the creation of an FM-index of raw, next generation sequencing data to enable rapid and flexible sequence queries.
We demonstrate the utility of these flexible queries performed as kmer (sequence substrings of length 'k') searches for two applications including SNP genotyping from whole genome sequencing, and viral detection from RNA-seq.
To learn more about FlexTyper, see our preprint on bioRxiv:
Demonstrating the utility of flexible sequence queries against indexed short reads with FlexTyper
For more information about FlexTyper, please refer to GitHubPages
OpenFlexTyper is installed with the install.sh script provided in the repository. Installation is currently supported for Linux operating systems.
The installation assumes that you have git installed.
Open a terminal and enter :
git clone https://github.com/wassermanlab/OpenFlexTyper.git
cd OpenFlexTyper
bash install.shThis repository comes with an example to test-run your installation and familiarize yourself with the usage of FlexTyper.
You can learn more about examples here
To design query files, follow the instructions in the fmformatter directory here
The output files from FlexTyper can be formatted into commonly used formats, e.g. VCF format with a basic genotyping methods.
To learn more, see the fmformatter directory here
Alice Kaye | Phillip Richmond | Jacques Kounkou | Tamar Av-Shalom
The MIT License (MIT)
Copyright (c) 2020, Wasserman lab
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