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. and Tangmunarunkit, H. 2017 Experiences with DERIVA: An Asset Management Platform for Accelerating eScience. IEEE 13th International Conference on e-Science (e-Science), Auckland, 2017, pp. 79-88, doi:10.1109/eScience.2017.20.

3. BDBag:

• D'Arcy, M., Chard, K., Foster, I., Kesselman, C., Madduri, R., Saint, N., & Wagner, R.. 2019. Big Data Bags: A Scalable Packaging Format for Science. Zenodo. doi:10.5281/zenodo.3338725.

4. 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.

5. trimgalore:

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

6. hisat2:

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

Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. 2019 Nat Biotechnol. Aug;37(8):907-915. doi:10.1038/s41587-019-0201-4.

7. samtools:

• Li H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, and 1000 Genome Project Data Processing Subgroup. 2009. The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25: 2078-9. doi:10.1093/bioinformatics/btp352

8. picard:

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

9. featureCounts:

• Liao, Y., Smyth, G.K., Shi, W. 2014 featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. Apr 1;30(7):923-30. doi:10.1093/bioinformatics/btt656.

10. 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/.

11. deeptools:

• Ramírez, F., D. P. Ryan, B. Grüning, V. Bhardwaj, F. Kilpert, A. S. Richter, S. Heyne, F. Dündar, and T. Manke. 2016. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research 44: W160-165. doi:10.1093/nar/gkw257

12. FastQC

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

13. MultiQC:

• Ewels P., Magnusson M., Lundin S. and 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

14. Nextflow:

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