BioDepot/RNA-seq-lambda: Rapid RNA-seq pipeline using AWS lambda functions for alignmen

Rapid RNA-seq pipeline using AWS lambda functions for alignment

Introduction The scripts stored in this repository enable the use of AWS lambda functions to align 640 million reads with bwa in under 3 minutes - a process that takes bwa 20 hours when executing optimised software using a single thread. An entire UMI RNA-seq pipeline converting fastq files to transcript counts takes under 20 minutes on a m4 4x large instance. This is 100x faster than the 30 hours needed for the original unoptimised pipeline and 12x faster than an optimised pipeline executed with 16 threads. The repo contains the scripts used to execute the pipeline. Additional files that…

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• Hannah Le

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