If you use EAGER, please cite

    1. Peltzer; G. Jäger; A. Herbig; S. Seitz; C. Kniep; J. Krause; K. Nieselt: EAGER: efficient ancient genome reconstruction (Genome Biology 2016, 17:60, doi:10.1186/s13059-016-0918-z)

The project URL is:

Tools & Methods

  • Andrews, S. (2010). FastQC: A quality control tool for high throughput sequence data. Reference Source.
  • Daley, T., & Smith, A. D. (2013). Predicting the molecular complexity of sequencing libraries. Nature Methods, 10(4), 325–7. doi:10.1038/nmeth.2375
  • Ginolhac, A., Rasmussen, M., Gilbert, M. T. P., Willerslev, E., & Orlando, L. (2011). mapDamage: testing for damage patterns in ancient DNA sequences. Bioinformatics (Oxford, England), 27(15), 2153–5. doi:10.1093/bioinformatics/btr347
  • Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009). Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol, 10(3), R25. doi:10.1186/gb-2009-10-3-r25
  • Korneliussen, T. S., Albrechtsen, A., & Nielsen, R. (2014). ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics, 15(1), 356. doi:10.1186/s12859-014-0356-4
  • Li, H. (2013). Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv Preprint arXiv:1303.3997.
  • Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford, England), 25(14), 1754–60. doi:10.1093/bioinformatics/btp324
  • Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., … Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics (Oxford, England), 25(16), 2078–9. doi:10.1093/bioinformatics/btp352
  • Lunter, G., & Goodson, M. (2011). Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Research, 21(6), 936–9. doi:10.1101/gr.111120.110
  • McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., … DePristo, M. A. (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297–303. doi:10.1101/gr.107524.110
  • Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2.
  • Okonechnikov, K., Conesa, A., & García-Alcalde, F. (2016). Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics (Oxford, England), 32(2), 292–4. doi:10.1093/bioinformatics/btv566
  • Renaud, G., Slon, V., Duggan, A. T., & Kelso, J. (2015). Schmutzi: estimation of contamination and endogenous mitochondrial consensus calling for ancient DNA. Genome Biology, 16(1), 224. doi:10.1186/s13059-015-0776-0