Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference |
Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Drosophila subobscura male and female) | 14011–0131.10 | National Drosophila Species Stock Center (Cornell University) | stock center number: 14011–0131.10 | |
| Strain, strain background (Drosophila pseudoobscura male and female) | MV2-25 | National Drosophila Species Stock Center (Cornell University) | stock center number: 14011–0121.94 | |
| Biological sample (Drosophila lowei) | Jillo6 | isofemale line (deceased) | ||
| Biological sample (Drosophila athabasca EA) | PA60 | isofemale line (deceased) | ||
| Biological sample (Drosophila athabasca EB) | NJ28 | isofemale line (deceased) | ||
| Commercial assay or kit | TruSeq Stranded RNA kit | Illumina | cat # 20020595 | |
| Commercial assay or kit | TruSeq DNA Nano Prep kit | Illumina | cat # 20015965 | |
| Commercial assay or kit | DNeasy Kit | Qiagen | cat # 69504 | |
| Commercial assay or kit | Blood and Cell Culture DNA Midi Kit | Qiagen | cat # 13343 | |
| Commercial assay or kit | Gentra Puregene Tissue Kit | Qiagen | cat # 158667 | |
| Commercial assay or kit | Ligation sequencing kit | Nanopore | SQK-LSK108 | |
| Commercial assay or kit | Rapid sequencing kit | Nanopore | SQK-RAD004 | |
| Commercial assay or kit | Quick DNA plus Midi kit | Zymo | cat # D4075 | |
| Commercial assay or kit | Ligation sequencing kit | Nanopore | SQK-LSK109 | |
| Commercial assay or kit | SMARTer Universal Low Input DNA-seq kit | Takara/Rubicon Bio | R400676 | |
| Chemical compound, drug | H3K9me3 antibody | Diagenode | ||
| Software, algorithm | canu | Koren et al., 2017 | ||
| Software, algorithm | MUMmer | Kurtz et al., 2004 | ||
| Software, algorithm | WTDBG2 | Ruan and Li, 2019 | ||
| Software, algorithm | minimap2 | Li, 2018 | ||
| Software, algorithm | Bandage | Wick et al., 2015 | ||
| Software, algorithm | BWA | Li and Durbin, 2009 | ||
| Software, algorithm | SAMtools | Li et al., 2009 | ||
| Software, algorithm | bedtools | Quinlan and Hall, 2010 | ||
| Software, algorithm | QUIVER | Chin et al., 2013 | ||
| Software, algorithm | PILON | Walker et al., 2014 | ||
| Software, algorithm | RACON | Vaser et al., 2017 | ||
| Software, algorithm | Juicebox | Durand et al., 2016a | ||
| Software, algorithm | Juicer | Durand et al., 2016b | ||
| Software, algorithm | 3D-DNA | Dudchenko et al., 2017 | ||
| Software, algorithm | GATK UnifiedGenotyper | DePristo et al., 2011 | ||
| Software, algorithm | REPdenovo | Chu et al., 2016 | ||
| Software, algorithm | RepeatMasker | Smith et al., 2005 | ||
| Software, algorithm | MAKER | Campbell et al., 2014 | ||
| Software, algorithm | HiSat2 | Kim et al., 2015 | ||
| Software, algorithm | StringTie | Pertea et al., 2015 | ||
| Software, algorithm | BUSCO | Simão et al., 2015 | ||
| Software, algorithm | Tandem Repeat Finder | Benson, 1999 | ||
| Software, algorithm | k-Seek | Wei et al., 2014; https://github.com/weikevinhc/k-seek | ||
| Software, algorithm | TideHunter | Gao et al., 2019 |