| Critical commercial assays |
|
| MagAttract HMW DNA kit |
Qiagen, Germany |
Cat #:67563 |
| KAPA HyperPlus Kit |
Roche |
Cat #:0896385001 |
| myBaits Custom DNA-seq kit |
Arbor Biosciences |
Cat #:300596.v5 |
| dsDNA HS Assay Kit |
ThermoFisher Scientific |
Cat #:Q32851
|
| Quantifast Sybr Green PCR MasterMix |
Qiagen |
Cat #: 204054 |
|
| Deposited data |
|
| Target capture genotypes |
This paper |
DRYAD: https://doi.org/10.5061/dryad.2bvq83bsm
|
| DArTseq data genotypes |
This paper |
DRYAD: https://doi.org/10.5061/dryad.2bvq83bsm
|
| Tasmanian devil reference genome mSarHar1.11 |
Ensembl |
Ensembl: GCF_902635505.1 https://asia.ensembl.org/Sarcophilus_harrisii/Info/Index
|
|
| Oligonucleotides |
|
| Probes for custom target capture baits |
This paper |
Supplementary Data 1 and DRYAD (https://doi.org/10.5061/dryad.2bvq83bsm) |
|
| Software and algorithms |
|
| Stacks v2.53 |
Catchen et al., 2013; Catchen et al., 2011
|
https://catchenlab.life.illinois.edu/stacks/ |
| FastQC |
Andrews, 2010 |
https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| MultiQC |
Ewels et al., 2016 |
https://multiqc.info/ |
| Trimmomatic v0.38 |
Bolger, Lohse & Usadel, 2014 |
http://www.usadellab.org/cms/?page=trimmomatic |
| Picard v2.18.4 |
Broad Institute Github Repository |
https://broadinstitute.github.io/picard/ |
| ngsCAT v0.1 |
López-Domingo et al., 2014 |
http://ngscat.clinbioinfosspa.es/start |
| GATK v4.1.9.0 |
McKenna et al., 2010 |
https://gatk.broadinstitute.org/hc/en-us |
| PHASE v2.1.1 |
Stephens and Scheet, 2005; Stephens et al., 2001
|
http://stephenslab.uchicago.edu/phase/download.html |
| BEDTools v2.25.0 |
Quinlan & Hall, 2010 |
https://bedtools.readthedocs.io/en/latest/ |
| VCFtools v0.1.14 |
Danecek et al., 2011 |
http://vcftools.sourceforge.net/man_latest.html |
| SAMtools v1.7 |
Li et al., 2009 |
http://www.htslib.org/ |
| BWA v0.7.17 |
Li & Durbin, 2009 |
http://bio-bwa.sourceforge.net/ |
| R v4.1.1 |
|
https://cran.r-project.org/bin/windows/base/ |
| GenAlEx v6.502 |
Peakall & Smouse, 2006; Peakall & Smouse, 2012
|
https://biology-assets.anu.edu.au/GenAlEx/Welcome.html |
| NeEstimator v2.1 |
Do et al., 2014 |
http://www.molecularfisherieslaboratory.com.au/neestimator-software/ |
|
fastSTRUCTURE v1.0 |
Raj, Stephens & Pritchard, 2014 |
https://bio.tools/faststructure |
| PMx |
Lacy, Ballou & Pollak, 2012 |
https://scti.tools/pmx/ |
|
| Other |
|
| Illumina NovaSeq 6000 |
Illumina |
|
| Illumina HiSeq 2000 |
Illumina |
|
