jdblischak

Comparing speed for yeast RNA-seq analysis - kallisto vs. Subread

Introduction

[kallisto][] is a new method for processing RNA-seq data. By pseudoaligning reads to a transcriptome instead of aligning reads to a genome, the quantification step is much faster. While the computational speedup will be huge for projects with many samples and/or with organisms with large genomes, I was curious how much time would be saved using [kallisto][] on a small RNA-seq project for an organism with a smaller genome. To perform this comparison, I downloaded 6 fastq files from a recent yeast RNA-seq study on GEO. I chose [Subread][subread] as the comparison method because it performs read alignment but is optimized for quickly obtaining gene counts (it soft clips reads instead of trying to map exact exon-exon boundaries).

yamaya

# Xcode 4.3.3
Apple clang version 3.1 (tags/Apple/clang-318.0.61) (based on LLVM 3.1svn)
Target: x86_64-apple-darwin11.4.0
Thread model: posix

# Xcode 4.3.2
Apple clang version 3.1 (tags/Apple/clang-318.0.58) (based on LLVM 3.1svn)
Target: x86_64-apple-darwin11.4.0
Thread model: posix

LukasKnuth

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