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VNTRseek is a computational pipeline for the detection of VNTRs. Given an input reference set of TRs and a set of next-generation sequencing reads, such as those produced by Illumina, VNTRseek produces a database and a VCF file with VNTR calls.
Currently, input reads in FASTA and FASTQ format are supported. Files must be compressed either using plain gzip (.gz) or gzip then tar (.tar.gz). BAM support is planned.
VNTRseek is also capable of running on clusters, though only the Grid Engine queuing system has been tested. Support for other platforms as pull requests is welcome.
The current release is version 1.09.2. Version 1.10 is being developed and adds the following:
- Drops MySQL dependency in favor of SQLite
- Adds a script to convert your MySQL databases to SQLite
- And more!
Please browse the rest of the documentation, in particular the Requirements section which details the software needed to build and install VNTRseek.
- Only CentOS 6 and Ubuntu 12.10 and up have been tested.
- Only a Linux 64-bit version of our software is available at this time.
- Currently, the default install path is valid only on UNIX-like platforms.