BFAST protocols

BFAST computational protocol

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 IN pipelines

PMCID: 5869567
PMID: 29610665
DOI: 10.1002/prp2.386

[…] 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: 5063418
PMID: 27736905
DOI: 10.1371/journal.pone.0163954

[…] using the solid platform. following filtering and processing, 68–76% of all rna sequence reads were mapped to the mouse reference genome assembly mm9 using an in-house pipeline that utilizes bfast (0.7.0a). unique reads with no more than two mismatches identified 12,168 genes representing the nsc-34 transcriptome. edger was used to calculate differences in gene expression levels […]

PMCID: 4378619
PMID: 25680078
DOI: 10.1371/journal.pgen.1004999

[…] 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: 4433240
PMID: 25978409
DOI: 10.1371/journal.pgen.1005221

[…] direct wgs (for jj2, jj5, jj7, jj50, jj52 and jj70) or snp-wgs (for jj49, jj57, jj62, jj69, jj71, jj73, jj78 and jj83), sequence data were aligned to c. elegans reference genome version ws220 using bfast [88] with default parameters. snp calling was performed by samtools [89]. a valid snp call required a minimum read depth of three. annovar [90] was used for annotation of snp coding potential. […]

PMCID: 4069013
PMID: 24959832
DOI: 10.1371/journal.pone.0099798

[…] captured by a customized nimblegen capture array and then sequenced using the abi solid v4.0 platform. the raw short reads were aligned to the reference human genome (ncbi genome build 36, hg18) by bfast.[22] samtools[23] was used to pile up aligned reads and call variants with quality filters. the resulting data were then subjected to quality control (qc) procedures, including variant-level […]

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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