Shout out to all the authors of these papers and packages!
Quentin Szabo et al. ,TADs are 3D structural units of higher-order chromosome organization in Drosophila.Sci.
Adv.4,eaar8082(2018).DOI:10.1126/sciadv.aar8082
Kruse, K., Hug, C.B. & Vaquerizas, J.M.
FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data.
Genome Biol 21, 303 (2020).
https://doi.org/10.1186/s13059-020-02215-9
https://github.com/LUMC/fastqsplitter/
- Langmead B, Wilks C., Antonescu V., Charles R. __[Scaling read aligners to hundreds of threads on general-purpose processors](https://doi.org/10.1093/bioinformatics/bty648)__. [Bioinformatics](https://academic.oup.com/bioinformatics). bty648.
- Langmead B, Salzberg S. __[Fast gapped-read alignment with Bowtie 2](http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1923.html)__. [Nature Methods](http://www.nature.com/nmeth). 2012, 9:357-359.
- Langmead B, Trapnell C, Pop M, Salzberg SL. __[Ultrafast and memory-efficient alignment of short DNA sequences to the human genome](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2009-10-3-r25)__. [Genome Biology](https://genomebiology.biomedcentral.com/) 10:R25.
- Aug. 2014 (BDGP Release 6 + ISO1 MT/dm6)
- (dm6, The FlyBase Consortium/Berkeley Drosophila Genome Project/Celera Genomics)