Source package for the core BCV executables:
To build them, you will need Boost Libraries Version 1.44 or later. See the README file in the archive for installation instructions.
bcvproc relies on the following two packages for preliminary processing of chromatogram files:
ttuner executable from this package processes chromatogram trace files in ABI format, calls pure and mixed bases, evaluates quality values and outputs the results in .phd, .scf and .poly files.
This tool is used to further process files generated by TraceTuner. It produces two files, containig physical properties (.fpoly) and p-values (.bqs) for each peak in a chromatogram. The package has been modified to output additional information required by bcvproc (the original version is available here).
For indel detection, the bcv_indel.pl script must be called after running bcvproc to obtain the final results. This script is part of bcvrun package:
The package also includes bcv_run.pl script that provides a higher level interface to the BCV pipeline, automatically calling TraceTuner, PolyScan and bcvproc applications.
You will also need to install these two packages:
bcvrun package depends on this Perl module to parse chromatogram file generated by Applied Biosystems (ABI) automated DNA sequencer. The original version has a bug that has been fixed in this distribution.
A multiple sequence alignment tool used by both bcvproc executable and bcvrun scripts.
Several environment variables must be set so that BCV modules will be able to run external applications:
export TTUNERCMD=/shell/command/to/run/ttuner
export POLYSCANCMD=/shell/command/to/run/polyscan
export BCVCMD=/shell/command/to/run/bcvproc
export MSACMD=/shell/command/to/run/muscle
Under Cygwin an additional setting may be required:
export LC_ALL="C"