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.
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]