KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER | |
|---|---|---|---|
| Chemicals, Peptides, and Recombinant Proteins | |||
| Pfu Turbo Cx Hotstart DNA Polymerase | Agilent Technologies |
6GG412 | |
| Herculase II Fusion DNA Polymerase | Agilent Technologies |
6GG679 | |
| 2x HI-RPM hybridization buffer | Agilent Technologies |
519G-G4G3 | |
| 0.5 M EDTA pH 8.0 | BioExpress | E177 | |
| Sera-Mag™ Magnetic Speed-beads™ | GE LifeScience | 651521G5G5G25G | |
| USER enzyme | New Biolabs | England | M55G5 |
| UGI | New Biolabs | England | MG281 |
| Bst DNA Polymerase2.0, large frag. | New Biolabs | England | MG537 |
| PE buffer concentrate | Qiagen | 19G65 | |
| Proteinase K | Sigma Aldrich | P6556 | |
| Guanidine hydrochloride | Sigma Aldrich | G3212 | |
| 3M Sodium Acetate (pH 5.2) | Sigma Aldrich | S1B99 | |
| Water | Sigma Aldrich | W4502 | |
| Tween-20 | Sigma Aldrich | P9416 | |
| Isopropanol | Sigma Aldrich | 650441 | |
| Ethanol | Sigma Aldrich | E1023 | |
| 5M NaCl | Sigma Aldrich | S5150 | |
| 1M NaOH | Sigma Aldrich | 11463 | |
| 20% SDS | Sigma Aldrich | 5030 | |
| PEG-8000 | Sigma Aldrich | B9510 | |
| 1 M Tris-HCl pH 8.0 | Sigma Aldrich | AM9B56 | |
| dNTP Mix | Thermo Scientific | Fisher | R1121 |
| ATP | Thermo Scientific | Fisher | R0441 |
| 10x Buffer Tango | Thermo Scientific | Fisher | BY5 |
| T4 Polynucleotide Kinase | Thermo Scientific | Fisher | EK0032 |
| T4 DNA Polymerase | Thermo Scientific | Fisher | EP0062 |
| T4 DNA Ligase | Thermo Scientific | Fisher | EL0011 |
| Maxima SYBR Green kit | Thermo Scientific | Fisher | K0251 |
| 50x Denhardt’s solution | Thermo Scientific | Fisher | 15001B |
| SSC Buffer (20x) | Thermo Scientific | Fisher | AM9110 |
| GeneAmp 10x PCR Gold Buffer | Thermo Scientific | Fisher | 4319B14 |
| Dynabeads MyOne Streptavidin T1 | Thermo Scientific | Fisher | 65602 |
| Salmon sperm DNA | Thermo Scientific | Fisher | 15632-011 |
| Human Cot-I DNA | Thermo Scientific | Fisher | 15219011 |
| DyNAmo HS SYBR Green qPCR Kit | Thermo Scientific | Fisher | F410L |
| Methanol, certified ACS | VWR | EM-MX04B5-3 | |
| Acetone, certified ACS | VWR | BDH1101-4LP | |
| Dichloromethane, certified ACS | VWR | EMD-DX0B35-3 | |
| Hydrochloric acid, 6N, 0.5N & 0.01N | VWR | EMD-HX0603-3 | |
| Critical Commercial Assays | |||
| High Pure Extender from Viral Nucleic Acid Large | Roche | 5114403001 | |
| MinElute PCR Purification Kit | Qiagen | 28006 | |
| NextSeq® 500/550 High Output Kit v2 (150 cycles) | Illumina | FC-404-2002 | |
| HiSeq® 4000 SBS Kit (50/75 cycles) | Illumina | FC-410-1001/2 | |
| Software and Algorithms | |||
| Samtools | (Li, 2011; Li et al., 2009) | http://samtools.sourceforge.net/ | |
| BWA | (Li and Durbin, 2009) | http://bio-bwa.sourceforge.net/ | |
| ADMIXTOOLS | (Patterson et al., 2012) | https://github.com/DReichLab/AdmixTools | |
| SeqPrep | https://github.eom/jstjohn/SeqPrep | https://github.com/jstjohn/SeqPrep | |
| bamrmdup | https://bitbucket.org/ustenzel/biohazard | https://bitbucket.org/ustenzel/biohazard | |
| AdapterRemovalv2 | (Schubert et al., 2016) | https://github.com/MikkelSchubert/adapterremoval | |
| Dedeup | (Peltzer et al., 2016) | https://eager.readthedocs.io/en/latest/ | |
| smartpca | (Patterson et al., 2006) | https://www.hsph.harvard.edu/alkes-price/software/ | |
| ADMIXTURE | (Alexander et al., 2009) | https://www.genetics.ucla.edu/software/admixture/download.html | |
| PMDtools | (Skoglund et al., 2014) | https://github.com/pontussk/PMDtools | |
| Haplofind 2 | (Vianello et al., 2013) | https://haplofind.unibo.it | |
| Haplogrep | (Kloss-Brandstätter et al., 2011; Weissensteiner et al., 2016) | http://haplogrep.uibk.ac.at/index.html | |
| Yfitter | https://sourceforge.net/projects/yfitter/ | https://sourceforge.net/projects/yfitter/ | |
| ContamMix | (Fu et al., 2013) | https://github.com/DReichLab/ADNA-Tools | |
| ANGSD | (Korneliussen et al., 2014) | https://github.com/ANGSD/angsd | |
| MEGA6 | (Tamura et al., 2013) | https://www.megasoftware.net | |
| mapDamage2.0 | (Jonsson et al., 2013) | https://ginolhac.github.io/mapDamage/ | |
| Geneious | https://www.geneious.com/ | https://www.geneious.com/ | |
| MUSCLE | (Edgar, 2004) | https://www.drive5.com/muscle/ | |
| FigTree | http://tree.bio.ed.ac.uk/software/ | http://tree.bio.ed.ac.uk/software/ | |
| PLINK2 | (Chang et al., 2015) | https://www.cog-genomics.org/plink/2.0/ | |
| ContamLD | (Nakatsuka et al., 2020) | https://github.com/nathan-nakatsuka/ContamLD | |
| Deposited Data | |||
| Sequencing Data | European Nucleotide Archive | PRJEB37446 | |
| Genotype Data | Reich Lab website | https://reich.hms.harvard.edu/datasets | |