BFC protocols

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BFC specifications

Information


Unique identifier OMICS_08402
Name BFC
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Heng Li <>

Publication for BFC

BFC in pipelines

 (2)
2017
PMCID: 5552988
PMID: 28798179
DOI: 10.1128/genomeA.00768-17

[…] were then sequenced in two miseq runs (2- × 150- and 2- × 250-bp run settings). nextera adapter trimming was performed using seqpurge and the trimmed reads were subsequently error corrected with bfc (, ). the adapter-trimmed and error-corrected paired-end reads were assembled using spades version 3.10 in the careful mode (). the average nucleotide identity was calculated using the online […]

2016
PMCID: 5073096
PMID: 27818652
DOI: 10.3389/fmicb.2016.01664

[…] xt kit (v3 chemistry) according to manufacturer's instructions producing 300 bp paired end reads. subsequent raw sequence data was assessed using fastqc. the reads were error corrected using the bfc algorithm before a relaxed quality trim using a sliding window as implemented in trimmomatic v0.33 (bolger et al., ; li, ). de novo genome assemblies were produced using spades assembler v3.6.2 […]


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BFC in publications

 (6)
PMCID: 5737690
PMID: 29186370
DOI: 10.1093/gbe/evx242

[…] are for paired-end read data for g. morbida from ., these values are for mate-pair read data for g. morbida from ., the raw paired-end reads for g. flava and g. putterillii were corrected using bfc (version r181) (). bfc utilizes a combination of hash table and bloom-filter to count k-mers for a given read and correct errors in that read based on the k-mer support. because bfc requires […]

PMCID: 5660112
PMID: 29109700
DOI: 10.3389/fmicb.2017.01913

[…] 11 k. pneumoniae and sequenced on the hiseq platform (illumina). the quality of the reads was assessed using fastqc (version 0.11.5; marçais and kingsford, ). error correction was performed using bfc (version r181; li, ). a relaxed quality trim was performed using trimmomatic (version 0.36) before the genome was de novo assembled using spades (version 3.9.1; bankevich et al., ; bolger et al., […]

PMCID: 5563063
PMID: 28821237
DOI: 10.1186/s12859-017-1784-8

[…] is further guided by using the per-base quality scores. many standalone read error correction algorithms and implementations have been proposed for illumina data, including ace [], bayeshammer [], bfc [], bless [], bless 2 [], blue [], ec [], fiona [], karect [], lighter [], musket [], pollux [], quake [], quorum [], racer [], sga-ec [] and trowel []. for a comprehensive overview […]

PMCID: 5364921
PMID: 28348924
DOI: 10.7717/peerj.3006

[…] run with several other unrelated libraries prepared with different truseq adaptors., the script used to analyse the dataset is provided in . illumina forward and reverse reads were denoised using bfc (), an error correcting tool designed specifically for illumina short reads. denoised paired reads were merged into contigs in usearch 8.1 () allowing for a maximum of five mismatches […]

PMCID: 5073096
PMID: 27818652
DOI: 10.3389/fmicb.2016.01664

[…] xt kit (v3 chemistry) according to manufacturer's instructions producing 300 bp paired end reads. subsequent raw sequence data was assessed using fastqc. the reads were error corrected using the bfc algorithm before a relaxed quality trim using a sliding window as implemented in trimmomatic v0.33 (bolger et al., ; li, ). de novo genome assemblies were produced using spades assembler v3.6.2 […]


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BFC institution(s)
Broad Institute, Cambridge, MA, USA
BFC funding source(s)
NHGRI U54HG003037; NIH GM100233

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