Difference between revisions of "WHAM"
m (Text replace - "([= ])[Mm]apping," to "$1Read mapping,") |
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{{Bioinformatics application | {{Bioinformatics application | ||
|sw summary=WHAM is a high-throughput sequence alignment tool. | |sw summary=WHAM is a high-throughput sequence alignment tool. | ||
− | |bio method=Read mapping, | + | |bio method=Read mapping, |
− | |bio tech=Illumina, | + | |bio tech=Illumina, |
− | |created at=University of Wisconsin-Madison, | + | |created at=University of Wisconsin-Madison, |
|maintained=Yes | |maintained=Yes | ||
− | |input format=FASTA, FASTQ, | + | |email address=yinan@cs.wisc.edu |
− | |output format=SAM, | + | |input format=FASTA, FASTQ, |
− | |licence=GPLv3, | + | |output format=SAM, |
+ | |licence=GPLv3, | ||
}} | }} | ||
== Description == | == Description == |
Latest revision as of 19:47, 3 December 2015
Application data |
|
Principal bioinformatics method(s) | Read mapping |
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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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