Input File Requirements

Input read files

VNTRseek expects that your input read files be gzip (.gz) or .tar.gz archives, with the sequence format at the start of the name, followed by an underscore ('_'). For example, FASTA sequences should be named fasta_filename.gz, and similarly for FASTQ files.

If you do not wish to rename your files, or have a large number of them to rename, you can take advantage of symbolic links on UNIX systems.

The following example script can be run from a separate directory and given the path to your input files. It will then create links to them in the working directory in the naming scheme VNTRseek prefers:

#!/bin/bash

# Link your files from $inputFilesDir to the current
# directory, with a file name matching the VNTRseek
# scheme. You can modify this to read the variables
# from arguments instead.

# Change to the location of your input reads
inputFilesDir="/path/to/read/files"
# Uncomment the correct sequence format
#format="fasta"
format="fastq"

for readFile in "$inputFilesDir"/*.gz
do
    bName=$(basename "$readFile")
    ln -s "$readFile" ./"$format"_"$bName"
done

When running on multi-core machines such as clusters, you may wish to split your input files into many smaller files (eg, 1 million reads per file) so that multiple instances of the sequence processing binaries can run simultaneously.

At the moment, FASTA and FASTQ formats are the only formats supported. VNTRseek 1.09 will have BAM support. For other formats, please open an issue in our issue tracker.

Input reference TR files

VNTRseek requires three files for each set of reference TRs the user will work with. The first two, .seq and .leb36 files, can be downloaded from TRDB after preparing a reference set there.

The third, .indist file, is a list of all "indistinguishable" TRs, one per line, with a negative sign preceding each TR id. "Indistinguishables" are TRs that appear too similar to be reliably distinguished from one another. This file can be produced by the pipeline if the proper option is supplied, but may not produce the best indistinguishable set. In 1.09, a utility script is added which simplifies the production of a good indistinguishable set.