7. References

• Review article on genome erosion: Díez-del-Molino, D., Sánchez-Barreiro, F., Barnes, I., Gilbert, M.T.P., and Dalén, L. 2018. Quantifying Temporal Genomic Erosion in Endangered Species. Trends in Ecology & Evolution 33 (3): 176–85.
• Snakemake: Köster, J., and Rahmann, S. 2012. Snakemake—a Scalable Bioinformatics Workflow Engine. Bioinformatics 28 (19): 2520–22.
• RepeatModeler: Smit, A.F.A., and Hubley, R. 2008-2015. RepeatModeler Open-1.0. http://www.repeatmasker.org.
• RepeatMasker: Smit, A.F.A., Hubley, R. and Green, P. 2013-2015. RepeatMasker Open-4.0. http://www.repeatmasker.org.
• samtools: Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J. Homer, N., Marth, G., Abecasis, G., Durbin, R., and 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map Format and SAMtools. Bioinformatics 25 (16): 2078–79.
• BEDTools: Quinlan, A. R. 2014. BEDTools: The Swiss-Army Tool for Genome Feature Analysis. In: Current Protocols in Bioinformatics, edited by Bateman, A., Pearson, W.R., Stein, L.D., Stormo, G.D., and Yates, J.R., 47:11.12.1-11.12.34. Hoboken, NJ, USA: John Wiley & Sons, Inc.
• FastQC: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
• Fastp: Chen, S., Zhou, Y., Chen, Y., and Gu, J. 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34 (17): i884–i890.
• 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): 3047–48.
• bwa: Li, H., and Durbin, R. 2009. Fast and Accurate Short Read Alignment with Burrows–Wheeler Transform. Bioinformatics 25 (14): 1754–60.
• QualiMap2: Okonechnikov, K., Conesa, A., and García-Alcalde, F. 2016. Qualimap 2: Advanced Multi-Sample Quality Control for High-Throughput Sequencing Data. Bioinformatics 32 (2): 292–94.
• picard: https://broadinstitute.github.io/picard/
• GATK: McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K. et al. 2010. The Genome Analysis Toolkit: A MapReduce Framework for Analyzing next-Generation DNA Sequencing Data. Genome Research 20 (9): 1297–1303.
• mapDamage2: Jónsson, H., Ginolhac, A., Schubert, M., Johnson, P.L.F., and Orlando, L. 2013. MapDamage2.0: Fast Approximate Bayesian Estimates of Ancient DNA Damage Parameters. Bioinformatics 29 (13): 1682–84.
• bcftools: Li, H. 2011. A Statistical Framework for SNP Calling, Mutation Discovery, Association Mapping and Population Genetical Parameter Estimation from Sequencing Data. Bioinformatics 27 (21): 2987–93.
• mlRho: Haubold, B., Pfaffelhuber, P., and Lynch, M.. 2010. MlRho – a Program for Estimating the Population Mutation and Recombination Rates from Shotgun-Sequenced Diploid Genomes. Molecular Ecology 19 (s1): 277–84.
• plink: Chang, C.C., Chow, C.C., Tellier, L.C., Vattikuti, S., Purcell, S.M., and Lee, J.J. 2015. Second-Generation PLINK: Rising to the Challenge of Larger and Richer Datasets. GigaScience 4 (1).
• snpEff: Cingolani, P., Platts, A., Wang, L.L., Coon, M., Nguyen, T., Wang, L., Land, S.J., Lu, X., and Ruden, D.M.. 2012. A Program for Annotating and Predicting the Effects of Single Nucleotide Polymorphisms, SnpEff: SNPs in the Genome of Drosophila Melanogaster Strain w 1118 ; Iso-2; Iso-3. Fly 6 (2): 80–92.
• GERP++: Davydov, E. V., Goode, D. L., Sirota, M., Cooper, G. M., Sidow, A., and Batzoglou, S. 2010. Identifying a High Fraction of the Human Genome to Be under Selective Constraint Using GERP++. PLoS Computational Biology 6 (12): e1001025.