Robert R. Fitak1,2, Elmira Mohandesan2,3, Jukka Corander4-6, Adiya Yadamsuren7,8, Battsetseg Chuluunbat9, Omer Abdelhadi10, Abdul Raziq11, Peter Nagy12, Chris Walzer13,14, Bernard Faye15, Pamela A. Burger2,14
- Department of Biology, Duke University, Durham, NC 27708 USA.
- Institute of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210 Vienna, Austria.
- Institute for Evolutionary Anthropology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
- Wellcome Trust Sanger Institute, Hinxton, UK.
- Helsinki Institute for Information Technology, Department of Mathematics and Statistics, University of Helsinki, FIN-00014, Helsinki, Finland.
- Department of Biostatistics, University of Oslo, N-0317, Oslo, Norway.
- Institute of Remote Sensing and Digital Earth, Chinese Academy of Sciences, Jia No.20 North, DaTun road, ChaoYang District, Beijing, China.
- Mammalian Ecology Laboratory, Institute of General and Experimental Biology, Mongolian Academy of Sciences, Peace avenue-54b, Bayanzurh District, Ulaanbaatar, 210351, Mongolia.
- Laboratory of Genetics, Institute of General and Experimental Biology, Mongolian Academy of Sciences, Peace avenue-54b, Bayarzurh District, Ulaanbaatar, 210351, Mongolia.
- University of Khartoum, Department for Meat Sciences, Khartoum, Sudan.
- Camelait, Alain Farms for Livestock Production, Alain Dubai Road, Alain, United Arab Emirates.
- Farm and Veterinary Department, Emirates Industry for Camel Milk and Products, PO Box 294236, Dubai, Umm Nahad, United Arab Emirates.
- Wildlife Conservation Society, Wildlife Health Program, Bronx, New York, USA.
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, 1160, Vienna, Austria.
- CIRAD-ES, UMR 112, Campus International de Baillarguet, TA C/112A, 34398, Montpellier, France.
This GitHub repository contains a summary of the various code, software, and data analysis pipelines used for the aforementioned study of 25 camel genomes. The contents represented here are only to be used as an example and not intended to be comeprehensive. The authors make no representation about the suitability or accuracy of this code, software, or data for any purpose, and make no warranties, either expressed or implied, for a particular purpose or that the use of this software or data will not infringe any third party patents, copyrights, trademarks, or other rights. The code, software and data are provided "as is". All content is hereby registered under the GNU General Public License v2.0, see LICENSE. Any publication that significantly relies upon the use of the content generated herein shall appropriately cite:
Fitak et al. (in prep.) Genomic signatures of domestication in Old World camels. TBD
Read processing, trimming, and mapping
SNP Calling - including base and variant quality score recalibrations
Analysis of Genetic Structure (PCA & Admixture)
PSMC Demographic Reconstructions
Homogeneity/HKA Tests of Selection
Sliding window analysis of genetic diversity
Recreating demographic history using G-PHOCS (Incomplete and not used in the study)
| Program | Version | Citation |
|---|---|---|
| POPOOLATION | 1.2.2 | Kofler, R. et al. PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals. PLoS One 6, e15925 (2011). |
| BWA | 0.6.2 | Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760 (2009). |
| LASTZ | v1.02.00 | Harris, R.S. (2007) Improved pairwise alignment of genomic DNA. Ph.D. Thesis, The Pennsylvania State University. |
| PICARD | 1.89 | Picard Toolkit. Broad Institute, GitHub Repository. http://broadinstitute.github.io/picard/ (2018) |
| SAMTOOLS | 0.1.19 | Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078-2079 (2009). |
| GATK | 3.1-1 | Van der Auwera, G. A. et al. From FastQ data to high-confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr. Protoc. Bioinformatics 43, 11.10.11-33 (2013). |
| ANGSD | 0.563 | Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinformatics 15, 356 (2014). |
| QUALIMAP | 2.0.1 | Okonechnikov K., Conesa A., García-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics 32(2):292-4 (2015). |
| BEDTOOLS |
|
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010). |
| VCFTOOLS | 0.1.12b | Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. 2011. The variant call format and VCFtools. Bioinformatics. 27:2156–8. |
| BEDOPS | n/a | Neph, S. et al. BEDOPS: high-performance genomic feature operations. Bioinformatics 28, 1919-1920 (2012). |
| SNPRELATE | 1.10.1 | Zheng, X. et al. A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics 28, 3326-3328 (2012). |
| ADMIXTURE | 1.23 |
|
| PSMC | 0.6.4 | Li, H. & Durbin, R. Inference of human population history from individual whole-genome sequences. Nature 475, 493-496 (2011). |
| BLAST2GO | 3.0.8 | Conesa, A. et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674-3676 (2005). |
| INTERPROSCAN | 5.7.48 | Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236-1240 (2014). |
| TOPGO | 2.28.0 | Alexa, A. & Rahnenfuhrer, J. (R package version 2.28.0, 2016). |
| SNPEFF | 4.1a | Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 6(2), 80-92 (2012). |