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 0.1.5) of WHAM:

  • Supports paired-end reads
  • Supports up to 5 errors
  • Supports alignments with gaps
  • Supports quality scores for filtering invalid alignments, and sorting valid alignments
  • finds ALL 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.

How does WHAM compare to BWA and Bowtie

  • Here is a report comparing WHAM to BWA.
  • The comparison to Bowtie is in the main reference below.


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]


WHAM is supported by a grant IIS-1110948 from the National Science Foundation and a Fellowship from Facebook.

The WHAM Team

The WHAM team is: Yinan LiAllie Terrell and Jignesh M. Patel.