Difference between revisions of "BFAST"
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|sw summary=Blat-like Fast Accurate Search Tool. | |sw summary=Blat-like Fast Accurate Search Tool. | ||
|bio domain=Whole Genome Re-sequencing | |bio domain=Whole Genome Re-sequencing | ||
| − | |bio method=Mapping, Alignments, Genome Indexing, Colorspace, | + | |bio method=Mapping, Alignments, Genome Indexing, Colorspace, |
|bio tech=ABI SOLiD, Helicos, 454, Illumina, | |bio tech=ABI SOLiD, Helicos, 454, Illumina, | ||
|created by=Nils Homer, Stanley F. Nelson and Barry Merriman | |created by=Nils Homer, Stanley F. Nelson and Barry Merriman | ||
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|licence=GPL, | |licence=GPL, | ||
|os=Unix, Solaris | |os=Unix, Solaris | ||
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}} | }} | ||
BFAST facilitates the fast and accurate mapping of short reads to reference sequences. Some advantages of BFAST include: | BFAST facilitates the fast and accurate mapping of short reads to reference sequences. Some advantages of BFAST include: | ||
| − | + | * Speed: enables billions of short reads to be mapped quickly. | |
| − | + | * Accuracy: A priori probabilities for mapping reads with defined set of variants. | |
| − | + | * An easy way to measurably tune accuracy at the expense of speed. | |
Specifically, BFAST was designed to facilitate whole-genome resequencing, where mapping billions of short reads with variants is of utmost importance. | Specifically, BFAST was designed to facilitate whole-genome resequencing, where mapping billions of short reads with variants is of utmost importance. | ||
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Find BFAST at [http://bfast.sourceforge.net http://bfast.sourceforge.net] | Find BFAST at [http://bfast.sourceforge.net http://bfast.sourceforge.net] | ||
| + | {{Links}} | ||
| + | {{References}} | ||
| + | {{Link box}} | ||
Revision as of 17:21, 23 May 2010
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Application data |
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| Created by | Nils Homer, Stanley F. Nelson and Barry Merriman |
|---|---|
| Biological application domain(s) | Whole Genome Re-sequencing |
| Principal bioinformatics method(s) | Mapping, Alignments, Genome Indexing, Colorspace |
| Technology | ABI SOLiD, Helicos, 454, Illumina |
| Created at | University of California, Los Angeles |
| Maintained? | Yes |
| Input format(s) | FASTQ, QSEQ (Illumina), CSFASTA/CSQUAL (ABI SOLiD), compressed/uncompressed |
| Output format(s) | SAM, BAF |
| Software features | parallel execution, command line |
| Programming language(s) | C |
| Licence | GPL |
| Operating system(s) | Unix, Solaris |
Summary: Blat-like Fast Accurate Search Tool.
"Error: no local variable "counter" was set." is not a number.
BFAST facilitates the fast and accurate mapping of short reads to reference sequences. Some advantages of BFAST include:
- Speed: enables billions of short reads to be mapped quickly.
- Accuracy: A priori probabilities for mapping reads with defined set of variants.
- An easy way to measurably tune accuracy at the expense of speed.
Specifically, BFAST was designed to facilitate whole-genome resequencing, where mapping billions of short reads with variants is of utmost importance.
BFAST supports both Illumina and ABI SOLiD data, as well as any other Next-Generation Sequencing Technology (454, Helicos), with particular emphasis on sensitivity towards errors, SNPs and especially indels. Other algorithms take short-cuts by ignoring errors, certain types of variants (indels), and even require further alignment, all to be the "fastest" (but still not complete). BFAST is able to be tuned to find variants regardless of the error-rate, polymorphism rate, or other factors.
Find BFAST at http://bfast.sourceforge.net
Links
References
To add a reference for BFAST, enter the PubMed ID in the field below and click 'Add'.
Search for "BFAST" in the SEQanswers forum / BioStar or:
| Web Search | Wiki Sites | Scientific |
|---|---|---|
