What is WHAM

WHAM is a high-throughput sequence alignment tool developed at University of Wisconsin-Madison. It aligns short DNA sequences (reads) to the whole human genome at a rate of over 1500 million 60bps reads per hour, which is one to two orders of magnitudes faster than the leading state-of-the-art techniques. Here is a quick feature list for the current version (v 0.1.2) of WHAM:

• Supports paired-end reads
• Supports up to 5 mismatches
• Supports up to 3 gaps
• Supports quality scores for filtering invalid alignments, and sorting valid alignments
• Supports multi-threading
• Supports rich reporting modes
• Supports SAM format output

Curious about the name WHAM – it stands for Wisconsin’s High-throughput Alignment Method.

WHAM is released under the GPLv3 license. You can download the source code with sample data from the download page.

The WHAM Team

The WHAM team is: Yinan Li, Allie Terrell and Jignesh M. Patel.

Reference

If you need to cite WHAM, please use: “WHAM: A High-throughput Sequence Alignment Method, Y. Li, A. Terrel and J. M. Patel, In Proceedings of the ACM SIGMOD International Conference on Management of Data, SIGMOD 2011, Athens, Greece.” [pdf]

Support

WHAM is supported by a grant from the National Science Foundation.