references.md

References

1. python:

• Anaconda (Anaconda Software Distribution, https://anaconda.com)

2. DERIVA:

• Bugacov, A., Czajkowski, K., Kesselman, C., Kumar, A., Schuler, R. E., & Tangmunarunkit, H. (2017, October). Experiences with DERIVA: An asset management platform for accelerating eScience. In 2017 IEEE 13th International Conference on e-Science (e-Science) (pp. 79-88). IEEE. doi:10.1109/eScience.2017.20.

3. BDBag:

• Madduri, R., Chard, K., D’Arcy, M., Jung, S. C., Rodriguez, A., Sulakhe, D., ... & Foster, I. (2019). Reproducible big data science: A case study in continuous FAIRness. PloS one, 14(4), e0213013. doi:10.1371/journal.pone.0213013.

4. trimgalore:

• trimgalore https://github.com/FelixKrueger/TrimGalore

5. hisat2:

• Kim, D., Paggi, J. M., Park, C., Bennett, C., & Salzberg, S. L. (2019). Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature biotechnology, 37(8), 907-915. doi:10.1038/s41587-019-0201-4.

6. samtools:

• Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., ... & Durbin, R. (2009). The sequence alignment/map format and SAMtools. Bioinformatics, 25(16), 2078-2079. doi:10.1093/bioinformatics/btp352

7. picard:

• “Picard Toolkit.” 2019. Broad Institute, GitHub Repository. http://broadinstitute.github.io/picard/; Broad Institute

8. featureCounts:

• Liao, Y., Smyth, G. K., & Shi, W. (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), 923-930. doi:10.1093/bioinformatics/btt656.

9. deeptools:

• Ramírez, F., Ryan, D. P., Grüning, B., Bhardwaj, V., Kilpert, F., Richter, A. S., ... & Manke, T. (2016). deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic acids research, 44(W1), W160-W165. doi:10.1093/nar/gkw257

10. Seqtk:

• Seqtk https://github.com/lh3/seqtk

11. R:

• R Core Team 2014. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL:http://www.R-project.org/.

12. FastQC

• FastQC https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

13. SeqWho

• Bennett, C., Thornton, M., Park, C., Henry, G., Zhang, Y., Malladi, V. S., & Kim, D. (2021). SeqWho: Reliable, rapid determination of sequence file identity using k-mer frequencies. bioRxiv, 2021.2003.2010.434827. doi:10.1101/2021.03.10.434827

14. RSeQC:

• Wang, L., Wang, S., Li, W. 2012 RSeQC: quality control of RNA-seq experiments. Bioinformatics. Aug 15;28(16):2184-5. doi:10.1093/bioinformatics/bts356.

15. MultiQC:

• Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19), 3047-3048. doi:10.1093/bioinformatics/btw354

16. Nextflow:

• Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature biotechnology, 35(4), 316-319.