Search Results for "kallisto"
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Showing 2 open source projects for "kallisto"
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kallisto
Near-optimal RNA-Seq quantification
kallisto is a program for near-optimal quantification of transcript abundances from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the idea of using pseudoalignment to quickly determine reads and targets’ compatibility, with no need for alignment. According to benchmarks done on a Mac desktop computer, kallisto can quantify 30 million human bulk RNA-seq reads in less than 3 minutes with just the read sequences and a transcriptome... -
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hppRNA
A Snakemake-based handy parameter-free pipeline for RNA-Seq analysis
... six core-workflows such as (1) Tophat - Cufflink - Cuffdiff; (2) Subread - featureCounts - DESeq2; (3) STAR - RSEM - EBSeq; (4) Bowtie - eXpress - edgeR; (5) kallisto - sleuth; (6) HISAT - StringTie - Ballgown. Please cite the following paper when using this package: Dapeng Wang. hppRNA—a Snakemake-based handy parameter-free pipeline for RNA-Seq analysis of numerous samples. Briefings in Bioinformatics, Volume 19, Issue 4, 20 July 2018, Pages 622–626.
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