BFAST
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Application data |
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| Created by | Nils Homer, Stanley F. Nelson and Barry Merriman |
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| Biological application domain(s) | Whole genome resequencing |
| Principal bioinformatics method(s) | Read mapping, Sequence alignment, Genome indexing |
| Technology | ABI SOLiD, Helicos, 454, Illumina |
| Created at | University of California, Los Angeles |
| Maintained? | Yes |
| Input format(s) | FASTQ, QSEQ, CSFASTA/CSQUAL (ABI SOLiD), compressed/uncompressed |
| Output format(s) | SAM, BAF |
| Software features | parallel execution, command line |
| Programming language(s) | C |
| Interface type(s) | Command line |
| Resource type(s) | Command-line tool |
| Licence | GPL |
| Operating system(s) | Solaris, UNIX |
| Contact: | bfast-help@lists.sourceforge.net |
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.
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 |
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