Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data
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Rayan Chikhi | Hélène Touzet | Ségolène Caboche | Jean-Marc Aury | Benjamin Istace | Camille Marchet | Leandro Lima | Corinne Da Silva | Corinne Da Silva | R. Chikhi | J. Aury | H. Touzet | B. Istace | S. Caboche | L. Lima | C. Marchet | Leandro Lima | Ségolène Caboche
[1] Niranjan Nagarajan,et al. Fast and sensitive mapping of nanopore sequencing reads with GraphMap , 2016, Nature Communications.
[2] Fritz J Sedlazeck,et al. Piercing the dark matter: bioinformatics of long-range sequencing and mapping , 2018, Nature Reviews Genetics.
[3] Aaron R. Quinlan,et al. Poretools: a toolkit for analyzing nanopore sequence data , 2014, bioRxiv.
[4] Li Tong,et al. Evaluating the impact of sequencing error correction for RNA-seq data with ERCC RNA spike-in controls , 2016, 2016 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI).
[5] Arnaud Lefebvre,et al. ELECTOR: evaluator for long reads correction methods , 2019, bioRxiv.
[6] Eugene W. Myers,et al. Non Hybrid Long Read Consensus Using Local De Bruijn Graph Assembly , 2017, bioRxiv.
[7] Mourad Elloumi,et al. Efficient Hybrid De Novo Error Correction and Assembly for Long Reads , 2016, 2016 27th International Workshop on Database and Expert Systems Applications (DEXA).
[8] Thomas Hackl,et al. proovread: large-scale high-accuracy PacBio correction through iterative short read consensus , 2014, Bioinform..
[9] Niranjan Nagarajan,et al. INC-Seq: accurate single molecule reads using nanopore sequencing , 2016, bioRxiv.
[10] Liliana Florea,et al. Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads , 2015, GigaScience.
[11] Ruifeng Hu,et al. LSCplus: a fast solution for improving long read accuracy by short read alignment , 2016, BMC Bioinformatics.
[12] Meena Kishore Sakharkar,et al. Distributions of exons and introns in the human genome , 2004, Silico Biol..
[13] Shilin Chen,et al. IDP-denovo: de novo transcriptome assembly and isoform annotation by hybrid sequencing , 2018, Bioinform..
[14] Esko Ukkonen,et al. Accurate self-correction of errors in long reads using de Bruijn graphs , 2016, Bioinform..
[15] Piet Demeester,et al. Jabba: hybrid error correction for long sequencing reads , 2015, Algorithms for Molecular Biology.
[16] Feng Luo,et al. MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads , 2017, Nature Methods.
[17] Martin Vingron,et al. Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels , 2012, Bioinform..
[18] Junqi He,et al. NHERF1 Enhances Cisplatin Sensitivity in Human Cervical Cancer Cells , 2017, International journal of molecular sciences.
[19] Mark Akeson,et al. Nanopore Long-Read RNAseq Reveals Widespread Transcriptional Variation Among the Surface Receptors of Individual B cells , 2017 .
[20] Thomas D. Wu,et al. GMAP: a genomic mapping and alignment program for mRNA and EST sequence , 2005, Bioinform..
[21] Ergude Bao,et al. HALC: High throughput algorithm for long read error correction , 2017, BMC Bioinformatics.
[22] Helga Thorvaldsdóttir,et al. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..
[23] Sara Goodwin,et al. Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome , 2015, bioRxiv.
[24] Zhong Wang,et al. Next-generation transcriptome assembly , 2011, Nature Reviews Genetics.
[25] Tyson A. Clark,et al. Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing , 2015, Nucleic acids research.
[26] H. Schwender,et al. Validation of Splicing Events in Transcriptome Sequencing Data , 2017, International journal of molecular sciences.
[27] Xun Xu,et al. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads , 2013, Bioinform..
[28] M. Schatz,et al. Phased diploid genome assembly with single-molecule real-time sequencing , 2016, Nature Methods.
[29] Tyson A. Clark,et al. Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing , 2016, Nature Communications.
[30] J. Rinn,et al. Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs , 2010, Nature Biotechnology.
[31] Kresimir Krizanovic,et al. Evaluation of tools for long read RNA-seq splice-aware alignment , 2017, bioRxiv.
[32] J. Rinn,et al. Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs , 2010, Nature biotechnology.
[33] B. Haas,et al. Advancing RNA-Seq analysis , 2010, Nature Biotechnology.
[34] Gabor T. Marth,et al. SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications , 2012, PloS one.
[35] Stefan Engelen,et al. Genome assembly using Nanopore-guided Long and Error-free DNA reads , 2015 .
[36] Dominique Lavenier,et al. Evaluation of long read error correction software , 2017 .
[37] Kateryna D. Makova,et al. Deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon , 2018, Nature Communications.
[38] W. J. Kent,et al. BLAT--the BLAST-like alignment tool. , 2002, Genome research.
[39] Carl Kingsford,et al. Accurate assembly of transcripts through phase-preserving graph decomposition , 2017, Nature Biotechnology.
[40] Paolo Piazza,et al. Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis , 2017, F1000Research.
[41] Richard Mott,et al. EST_GENOME: a program to align spliced DNA sequences to unspliced genomic DNA , 1997, Comput. Appl. Biosci..
[42] Cédric Chauve,et al. LRCstats, a tool for evaluating long reads correction methods , 2017, Bioinform..
[43] S. Salzberg,et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads , 2015, Nature Biotechnology.
[44] Heng Li,et al. Minimap2: pairwise alignment for nucleotide sequences , 2017, Bioinform..
[45] Aaron A. Klammer,et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data , 2013, Nature Methods.
[46] M. Schatz,et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads , 2012, Nature Biotechnology.
[47] Helga Thorvaldsdóttir,et al. Integrative Genomics Viewer , 2011, Nature Biotechnology.
[48] Nanopore native RNA sequencing of a human poly(A) transcriptome , 2019, Nature Methods.
[49] S. Koren,et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.
[50] Mile Šikić,et al. Fast and accurate de novo genome assembly from long uncorrected reads , 2016, bioRxiv.
[51] Arnaud Lefebvre,et al. Hybrid correction of highly noisy long reads using a variable‐order de Bruijn graph , 2018, Bioinform..
[52] Scott J. Emrich,et al. HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning , 2017 .
[53] N. Loman,et al. A complete bacterial genome assembled de novo using only nanopore sequencing data , 2015, Nature Methods.
[54] N. Friedman,et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.
[55] Leena Salmela,et al. LoRDEC: accurate and efficient long read error correction , 2014, Bioinform..
[56] Steven J. M. Jones,et al. De novo assembly and analysis of RNA-seq data , 2010, Nature Methods.
[57] W. Wong,et al. Improving PacBio Long Read Accuracy by Short Read Alignment , 2012, PloS one.
[58] David L Adelson,et al. Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis , 2017, Cell Discovery.
[59] Cole Trapnell,et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.
[60] Jiannis Ragoussis,et al. Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations , 2016, Scientific Reports.
[61] Kin Fai Au,et al. A comparative evaluation of hybrid error correction methods for error-prone long reads , 2019, Genome Biology.