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      Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference

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          Abstract

          We introduce Salmon, a method for quantifying transcript abundance from RNA-seq reads that is accurate and fast. Salmon is the first transcriptome-wide quantifier to correct for fragment GC content bias, which we demonstrate substantially improves the accuracy of abundance estimates and the reliability of subsequent differential expression analysis. Salmon combines a new dual-phase parallel inference algorithm and feature-rich bias models with an ultra-fast read mapping procedure.

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          Most cited references 34

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          Fast gapped-read alignment with Bowtie 2.

          As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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            Is Open Access

            The Cancer Genome Atlas Pan-Cancer analysis project.

            The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile.
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              Near-optimal probabilistic RNA-seq quantification.

              We present kallisto, an RNA-seq quantification program that is two orders of magnitude faster than previous approaches and achieves similar accuracy. Kallisto pseudoaligns reads to a reference, producing a list of transcripts that are compatible with each read while avoiding alignment of individual bases. We use kallisto to analyze 30 million unaligned paired-end RNA-seq reads in <10 min on a standard laptop computer. This removes a major computational bottleneck in RNA-seq analysis.
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                Author and article information

                Journal
                101215604
                32338
                Nat Methods
                Nat. Methods
                Nature methods
                1548-7091
                1548-7105
                18 March 2017
                06 March 2017
                April 2017
                19 September 2017
                : 14
                : 4
                : 417-419
                Affiliations
                [1 ]Department of Computer Science, Stony Brook University
                [2 ]DNAnexus, 1975 W El Camino Real, Suite 101 Mountain View, CA 94040
                [3 ]Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Department of Biostatistics, Harvard TH Chan School of Public Health
                [4 ]Computational Biology Department, Carnegie Mellon University
                Author notes
                NIHMS849351
                10.1038/nmeth.4197
                5600148
                28263959

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                Life sciences

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