This is the official repository for VNTRseek. VNTRSeek is a computational pipeline for the detection of VNTRs. It was developed by Yevgeniy Gelfand et al in Dr. Gary Benson's Laboratory for Biocomputing and Informatics at Boston University.
C Perl C++ CMake Shell Makefile
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
cmake/Modules
perl
postinst
scripts
src
test
.gitignore
CLUSTER
CMakeLists.txt
COPYING
DetermineArch.cmake
FindDeps.cmake
HISTORY
INPUT
INSTALL.md
README.md
RUNNING
TARGETS
VCF example
deps
vs.cnf

README.md

Overview

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). Preliminary BAM support is available beginning with version 1.09.

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.

Documentation

The full documentation is located on the wiki on our GitHub page.

Download

The latest version of VNTRseek is 1.09.2. You can download it from the releases tab on our GitHub repo, or from our download page.