BICF SRA Downloading Pipeline
| Main Authors: | Jonathan R. Gesell, Jeremy A. Mathews, Venkat S. Malladi |
|---|---|
| Format: | info software |
| Terbitan: |
, 2020
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/3739789 |
Daftar Isi:
- This pipeline is a simple method for downloading bulk SRA data, and renaming it, and having it ready to use in our other Astrocyte pipelines BICF at UT Southwestern Dept. of Bioinformatics. The pipeline uses Nextflow, a bioinformatics workflow tool, to download multiple files with NCBI's SRA Toolkit simultaneously, speeding up the process. Once the files have been downloaded, it runs FastQC to check the individual file quality metrics, and MultiQC on the entire data set, once the downloads have finished. This pipeline was designed to use a SLURM setup, as used by the BioHPC Cluster, however should be adaptable to run on nearly any system using and supported by Nextflow. Pipeline is maintained at Git repository.