bryoinformatics/rna-seq repository overview

This container holds software used for the RNAseq pipeline to quantify transcript abundance from raw sequencing data (https://github.com/bryoinformatics/RNAseq⁠).

The following software are used in the pipeline:

• FastQC v0.12.1
• Trim Galore! v0.6.10
• Salmon v1.10.0

Citations:

• Andrews, S. (2019). FastQC: A quality control tool for high throughput sequence data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/⁠
• Krueger, F. (2023). Babraham Bioinformatics—Trim Galore! (v0.6.10). https://zenodo.org/badge/latestdoi/62039322⁠
• Patro, R., Duggal, G., Love, M. et al. (2017). Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 14, 417–419. https://doi.org/10.1038/nmeth.4197⁠