bryoinformatics/variant-id 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:

• BBMap v39.01
• bcftools v1.9
• FastQC v0.12.1
• GATK v4.3.0.0
• picard v2.27.5
• samtools v1.6
• Trim Galore! v0.6.10

Citations:

• Andrews, S. (2019). FastQC: A quality control tool for high throughput sequence data. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/⁠
• Broad Institute. (2022). “Picard.” Broad Institute, GitHub repository. http://broadinstitute.github.io/picard/⁠.
• Bushnell, B., Rood, J., & Singer, E. (2017). BBMerge – Accurate paired shotgun read merging via overlap. PLOS ONE, 12(10), e0185056. https://doi.org/10.1371/journal.pone.0185056⁠
• Bushnell, B. (2022). "BBMap." SourceForge repository. https://sourceforge.net/projects/bbmap/⁠
• Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M., & Li, H. (2021). Twelve years of SAMtools and BCFtools. GigaScience, 10(2), giab008. https://doi.org/10.1093/gigascience/giab008⁠
• Krueger, F. (2023). Babraham Bioinformatics—Trim Galore! (v0.6.10). https://zenodo.org/badge/latestdoi/62039322⁠
• Van der Auwera, G. A., & O’Connor, B. D. (2020). Genomics in the Cloud: Using Docker, GATK, and WDL in Terra (1st ed.). O’Reilly Media.