WHAM
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Application data |
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| Principal bioinformatics method(s) | Read mapping |
|---|---|
| Technology | Illumina |
| Created at | University of Wisconsin-Madison |
| Maintained? | Yes |
| Input format(s) | FASTA, FASTQ |
| Output format(s) | SAM |
| Licence | GPLv3 |
| Contact: | yinan@cs.wisc.edu |
Summary: WHAM is a high-throughput sequence alignment tool.
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Contents
Description
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.
Features
- 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.
Links
References
none specified
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| Web Search | Wiki Sites | Scientific |
|---|---|---|
