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BFC: correcting Illumina sequencing errors

Heng Li
2015 Bioinformatics  
BFC is a free, fast and easy-to-use sequencing error corrector designed for Illumina short reads.  ...  In evaluations on real data, BFC appears to correct more errors with fewer overcorrections in comparison to existing tools.  ...  INTRODUCTION Error correction is a process to fix sequencing errors on a sequence read by using other overlapping reads that do not contain the errors.  ... 
doi:10.1093/bioinformatics/btv290 pmid:25953801 pmcid:PMC4635656 fatcat:rzpgtoryqbcbvo7hgvct3nfcti

Correcting Illumina sequencing errors for human data [article]

Heng Li
2015 arXiv   pre-print
Summary: We present a new tool to correct sequencing errors in Illumina data produced from high-coverage whole-genome shotgun resequencing.  ...  This evaluation has the most complete collection of high-performance error correctors so far. Availability and implementation: https://github.com/lh3/bfc Contact: hengli@broadinstitute.org  ...  INTRODUCTION Error correction is a process to fix sequencing errors on a sequence read by using other overlapping reads that do not contain the errors.  ... 
arXiv:1502.03744v1 fatcat:ldjjxhdcdjaz5grtwyy3nthzgy

bfc, a novel serpent co-factor for the expression of croquemort, regulates efferocytosis in Drosophila melanogaster

Qian Zheng, Ning Gao, Qiling Sun, Xiaowen Li, Yanzhe Wang, Hui Xiao, Estee Kurant
2021 PLoS Genetics  
Here, we identified a novel gene bfc (booster for croquemort), which plays a role in efferocytosis, specifically the regulation of the crq expression.  ...  Overall, we show that Bfc serves as a Srp co-factor to upregulate the transcription of the crq encoded receptor, and consequently boosts macrophage efferocytosis in response to excessive apoptosis.  ...  The libraries were constructed and sequenced using a HiSeq 2500 system (Illumina), which generated ~21 million read pairs per sample.  ... 
doi:10.1371/journal.pgen.1009947 pmid:34860835 pmcid:PMC8673676 fatcat:4yw3gkjkxbhodhuesac2ttjd6q

Optimizing error correction of RNAseq reads [article]

Matthew D MacManes
2015 bioRxiv   pre-print
This manuscript evaluates several popular read-correction tool's ability to correct sequence errors commonplace to transcriptome derived Illumina reads.  ...  Motivation: The correction of sequencing errors contained in Illumina reads derived from genomic DNA is a common pre-processing step in many de novo genome assembly pipelines, and has been shown to improved  ...  Unlike the previous generation of sequence data (e.g., Sanger) where error rates were far below 1%, the rate of error typical of the Illumina platform is between 1% and 3% .  ... 
doi:10.1101/020123 fatcat:z5sv22fuura6tewu2drydvqla4

Comprehensive Evaluation of Error-Correction Methodologies for Genome Sequencing Data [chapter]

Yun Heo, Gowthami Manikandan, Anand Ramachandran, Deming Chen
2021 Bioinformatics  
Many tools exist for error correction of such sequencing data, improving the quality of downstream analyses.  ...  Next generation sequencing (NGS) technologies like Illumina and third generation sequencing (TGS) technologies like PacBio and Oxford Nanopore Technology use different techniques for sequencing and provide  ...  CONCLUSION Among the Illumina error-correction methods that were evaluated, ALLPATHS-LG, BFC, BLESS, Lighter, Quake, QuorUM, and SGA generated accurate results for over 30X read coverage.  ... 
doi:10.36255/exonpublications.bioinformatics.2021.ch6 fatcat:7lmnm7637vhepcdzu2xlkz3gfa

Comprehensive assessment of error correction methods for high-throughput sequencing data [article]

Yun Heo, Gowthami Manikandan, Anand Ramachandran, Deming Chen
2020 arXiv   pre-print
We also present a compilation of sequencing datasets for Illumina, PacBio and ONT platforms that present challenging scenarios for error-correction tools.  ...  Though many tools exist for error correction of sequencing data from NGS and TGS methods, no standard method is available yet to evaluate the accuracy and effectiveness of these error-correction tools.  ...  EVALUATION RESULTS FOR ILLUMINA ERROR CORRECTION TOOLS Accuracy of Illumina Error Correction Tools For I5, the largest input genome, ALLPATHS-LG, BFC, BLESS, Lighter, Musket, Quake, QuorUM, and SGA showed  ... 
arXiv:2007.05121v1 fatcat:7bq5pwcrubduxo3dpfcpiptxne

Evaluation of the impact of Illumina error correction tools on de novo genome assembly

Mahdi Heydari, Giles Miclotte, Piet Demeester, Yves Van de Peer, Jan Fostier
2017 BMC Bioinformatics  
Recently, many standalone applications have been proposed to correct sequencing errors in Illumina data.  ...  Results: For twelve recent Illumina error correction tools (EC tools) we evaluated both their ability to correct sequencing errors and their ability to improve de novo genome assembly in terms of contig  ...  Overall, Karect has the highest error correction gain for all datasets. For most datasets, BFC, SGA-EC and Trowel correct significantly fewer sequencing errors compared with other EC tools.  ... 
doi:10.1186/s12859-017-1784-8 pmid:28821237 pmcid:PMC5563063 fatcat:5rb3wd7gxnetjbz234qqwloeei

Even better correction of genome sequencing data [article]

Maciej Dlugosz and Sebastian Deorowicz and Marek Kokot
2017 arXiv   pre-print
We introduce an improved version of RECKONER, an error corrector for Illumina whole genome sequencing data. By modifying its workflow we reduce the computation time even 10 times.  ...  The correction algorithms are examined on huge data sets, i.e., human and maize genomes for both Illumina HiSeq and MiSeq instruments.  ...  The problem of sequencing errors can be partially solved by involving specialized correction algorithms. In the recent years many of them were developed.  ... 
arXiv:1703.00690v1 fatcat:5g63l3nc2jaajl7rgd2vnkgy6e

Illumina error correction near highly repetitive DNA regions improves de novo genome assembly

Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier
2019 BMC Bioinformatics  
Several standalone error correction tools have been proposed to correct sequencing errors in Illumina data in order to facilitate de novo genome assembly.  ...  Results: We propose BrownieCorrector, an error correction tool for Illumina sequencing data that focuses on the correction of only those reads that overlap short DNA patterns that are highly repetitive  ...  Recently, a number of standalone error correction (EC) tools have been proposed which aim to identify and correct errors in sequencing data: ACE [5] , BayesHammer [6] , BFC [7] , BLESS [8] , BLESS  ... 
doi:10.1186/s12859-019-2906-2 fatcat:5xxawaljwveovde3r44ly7x4cy

Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads

Li Song, Liliana Florea
2015 GigaScience  
Findings: We developed a k-mer based method, Rcorrector, to correct random sequencing errors in Illumina RNA-seq reads.  ...  Error correction methods have been highly effective for whole-genome sequencing (WGS) reads, but are unsuitable for RNA-seq reads, owing to the variation in gene expression levels and alternative splicing  ...  Findings We evaluate Rcorrector for its ability to correct Illumina sequencing reads, both simulated and real.  ... 
doi:10.1186/s13742-015-0089-y pmid:26500767 pmcid:PMC4615873 fatcat:3wkedi2nfrhdpifbqocmluwtw4

Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly

Katrin Sameith, Juliana G. Roscito, Michael Hiller
2016 Briefings in Bioinformatics  
A first step in genome assembly is to computationally correct sequencing errors. However, correcting all errors in these longer reads is challenging.  ...  Next-generation sequencers such as Illumina can now produce reads up to 300 bp with high throughput, which is attractive for genome assembly.  ...  In the past, short insert libraries were often sequenced with 2 Â 100 bp reads from Illumina HiSeq sequencers. Illumina technology now offers to sequence 2 Â 250 or even 2 Â 300 bp reads.  ... 
doi:10.1093/bib/bbw003 pmid:26868358 pmcid:PMC5221426 fatcat:dbzyh5iodzdjtn23vzavlc6iue

Benchmarking of computational error-correction methods for next-generation sequencing via unique molecular identifiers [article]

Keith Mitchell, Igor Mandric, Lana Martin, Mihai Pop, Serghei Mangul
2019 bioRxiv   pre-print
Computational error-correction promises to eliminate sequencing errors, but the relative performance of error correction algorithms remains unknown.  ...  We then performed a realistic evaluation of error correction methods.  ...  BFC: correcting Illumina sequencing errors. Bioinformatics 31 , 2885-2887 (2015). 21. Song, L., Florea, L. & Langmead, B.  ... 
doi:10.1101/642843 fatcat:rb4h5clo2vecdavoucuir24ynm

Instance-based error correction for short reads of disease-associated genes

Xuan Zhang, Yuansheng Liu, Zuguo Yu, Michael Blumenstein, Gyorgy Hutvagner, Jinyan Li
2021 BMC Bioinformatics  
Background Genomic reads from sequencing platforms contain random errors.  ...  Conclusion Instance-based strategy makes it possible to explore fine-grained patterns focusing on specific genes, providing high precision error correction and convincing gene sequence assembly.  ...  The most popular Illumina platforms generate sequencing data with 0.5-2.5% error rates [5] .  ... 
doi:10.1186/s12859-021-04058-y pmid:34078284 fatcat:lokry7hh4bhtjdafi3wvbicwaq

Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs [article]

Antoine Limasset, Jean-Francois Flot, Pierre Peterlongo
2018 arXiv   pre-print
This graph is filtered on the basis of k-mer abundance then of unitig abundance, thereby removing from most sequencing errors.  ...  The cleaned graph is then used as a reference on which the reads are mapped to correct them.  ...  As k-mer-spectrum correctors are usually geared towards correcting SGS reads, they use a k-mer size around 31 that is well suited for the error rate of Illumina data.  ... 
arXiv:1711.03336v2 fatcat:mdsod7nqsbfmdicgly7lgvudnq

Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs

2019 Bioinformatics  
This graph is filtered on the basis of k-mer abundance then of unitig abundance, thereby removing most sequencing errors.  ...  Despite much work on short-read correction, present-day correctors either do not scale well on large datasets or consider reads as mere suites of k-mers, without taking into account their full-length sequence  ...  Patterns of weak k-mers resulting from a sequencing error, depending on k. Sequencing errors in the read are pictured in grey.  ... 
doi:10.1093/bioinformatics/btz102 pmid:30785192 fatcat:bfnvztlenjcchnmmhjcfab7qlq
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