autoseq README

autoseq is a small package of base calling software for ABI automated DNA sequencers. It is intended as a starting point for researchers interested in new base calling algorithms. It implements a simple Bayesian peak identification algorithm which is experimental and does not generally perform better than software provided by ABI.

autoseq is written in C++. It is known to compile with g++ 2.7.2.1. The package includes C++ classes which represent ABI trace files, individual traces, and lists of picked peaks. A program called autoseq uses these classes to demonstrate base calling on real data from Bob Waterston's c. elegans sequencing project at Washington University.

This code is hereby released to the public domain. Comments, bug reports, and usage reports are appreciated. I do not impose any restrictions on its use. However, I will apprciate it if derived code references http://dasher.wustl.edu/~reece/autoseq/ primarily to advertise its availability.

autoseq was written as part of a Masters thesis in computer science at Washington University in St. Louis and the Institute for Biomedical Computing. Please note that I am now a graduate student in biophysics and am not actively developing autoseq. However, I will make a modest effort to keep updates available at the above site.

Get it right here, right now

* source code [gzip'd tar; 110 kb; pgp certificate]

Contains source for CTrace and CTraceFile which aid manipulation of automated sequencing data. CTracefile can read ABI raw and processed data, and read and write SCF (Standard Chromatogram Format) data. CPeakList implements a statistical model for peak assignment. autoseq is a command- line interface to the above objects which handles a variety of manipulation and analysis tasks.

* sample data [gzip'd tar; 524 kb; pgp certificate]

Contains the sample data described in the thesis.

* transformation matrices [gzip'd tar; 1 kb; pgp certificate]

Contains the matrices described in the thesis.

* thesis [gzip'd postscipt; 297 kb; pgp certificate]

Full Title: An Object-Oriented System for the Analysis of Automated DNA Sequencing Data.
Contains the thesis in PostScript format. The thesis describes the autoseq project, results, usage, etc. The above packages are sufficient to reproduce the results in this document.

* http://ibc.wustl.edu:70/1/c++-tools/ (may be outdated)

To use the PGP signatures, type something like:
$ pgp autoseq-thesis.tar.gz.sig autoseq-thesis.tar.gz

Click for more information on cryptography.