BFAST pipeline

BFAST specifications


Unique identifier OMICS_00652
Alternative name BLAT-like Fast Accurate Search Tool
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Barry Merriman <>

Publication for BLAT-like Fast Accurate Search Tool

BFAST citations

PMCID: 5869567

[…] each sequence was scanned for low‐quality reads and any read length of less than 35 bases was discarded to effectively eliminate low‐quality reads while retaining high‐quality regions. bfast was used as the primary sequence alignment algorithm employing a tophat‐like strategy to align sequencing reads that crossed splicing junctions. sequence reads were aligned to a filtering index […]

PMCID: 4378619

[…] the libraries were sequenced on solid 5500xl. the resulting 75 bp solid reads were mapped to saccharomyces cerevisiae reference genome saccer3 using in-house mapping pipelines that utilizes bfast-0.7.0a [81]. briefly, using our rna-seq pipeline, poor quality and rrna/trnas reads were first discarded. the remaining reads were mapped to reference genome saccer3 and a splice-junction […]

PMCID: 3204756

[…] snps. to be called an snp, the position had to have a minimum of 5× coverage. after eliminating any bases with a quality score <20 (as reported by solid) or a mapping score <40 (calculated by bfast), 90% of the reads had to agree. identified snps were then visually evaluated by viewing the wgs alignment in solscape, a short-read sequence-alignment viewer developed in house (j. pearson et […]

BFAST institution(s)
Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
BFAST funding source(s)
Partially supported by University of California Systemwide Biotechnology Research and Education Program GREAT Training Grant 2007-10, the NIH Neuroscience Microarray Consortium (U24NS052108), a supplement to a grant from the NIMH (R01 MH071852) and the Dani Saleh Brain Tumor Fund.

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