Welcome to dnaa.
Please see the file LICENSE for details.
Please see the file INSTALL for installation instructions;
This software package has limited support since it is in
== dkbaseencoding ==
This is a utility to evaluate k-base encoding. Typically,
on the ABI SOLiD system, we use 2-base encoding. We have
generalized this encoding to use k-bases. This program
will allow us to evaluate the sensitivity and accuracy of
using k-base encoding schmeme. A manuscript detailing our
results is available upon request.
== dtranslocations ==
This utility aids in the search for structural variants by
efficiently binning paired end reads. Given a binning
strategy we are able to find bins between two portions of
the reference that are over-represented.
== dutil ==
This directory consists of valuable utilities.
=== dbamerrordist ===
This utility calculates various error distributions after
mapping. This works particularly well when assessing ABI
SOLiD color space error rates versus its decoded error rate.
=== dbamfilter ===
This utility allows a BAM file to be filtere based on various
criteria. A integral feature is its PCR duplicate removal
feature and is meant to replace the "rmdup" command in
=== dbammetric ===
This utility is used to compute various metrics useful for
filtering. This is in active development.
=== dbampairedenddist ===
This utility is used to print the distribution of the
distance between paired-end reads using reads that have both
ends matching only one location on the same strand.
=== dbamstats ===
This utility is used to print mapping information about
the BAM file. This is meant to replace the cryptic SAMtools
=== drepeateanalyzer ===
This utility is used to analyze the number of bases that are
annotated as repeates in a BFAST aligned file (BAF).
== dqc ==
This utility creates summary statistics and plots for assessing
the pre-alignment and post-alignment quality of NGS data.