Concepedia

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

Brian J. Haas, Alexie Papanicolaou, Moran Yassour, Manfred Grabherr, Philip D. Blood, Joshua C. Bowden, Matthew Brian Couger, David Eccles, Bo Li, Matthias Lieber,

Nature Protocols · 2013 · 9.1K citations · 45 references

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45

Fast gapped-read alignment with Bowtie 2

Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations

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<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

Mark D. Robinson, Davis J. McCarthy, Gordon K. Smyth · Bioinformatics · 2009 · 44.5K citations · Full text

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Cutadapt removes adapter sequences from high-throughput sequencing reads

Marcel Martin · EMBnet journal · 2011 · 35.8K citations · Full text

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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Bo Li, Colin N. Dewey · BMC Bioinformatics · 2011 · 23.4K citations · Full text

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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Ben Langmead, Cole Trapnell, Mihai Pop et al. · Genome biology · 2009 · 23K citations · Full text

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