Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Oligonucleotides and Probes | ||
| DJ OligoMix - 5’ Biotin L | LC Sciences, LLC | Custom 100bp oligo paint corresponding to CHM13 chr13:5424523–5770548 |
| CenSat D14Z1/D22Z1 | Cytocell | LPE 014 |
| Human whole chromosome paint (chr15) | Applied Spectral Imaging | FPRPR0167 |
| 45S rDNA probe | Empire genomics | RP11–450E20 |
| Experimental models: Cell lines | ||
| CHM13 | Magee-Womens Hospital (Pittsburgh) IRB MWH-20–054 |
CHM13 |
| HG002 | Coriell Institute for Medical Research | GM24385 |
| GM03417 | Coriell Institute for Medical Research | GM03417 |
| GM03786 | Coriell Institute for Medical Research | GM03786 |
| GM04890 | Coriell Institute for Medical Research | GM04890 |
| HG01204 | Coriell Institute for Medical Research | HG01204 |
| HG00619 | Coriell Institute for Medical Research | HG00619 |
| HG00620 | Coriell Institute for Medical Research | HG00620 |
| HG01981 | Coriell Institute for Medical Research | HG01981 |
| HG01890 | Coriell Institute for Medical Research | HG01890 |
| HG01889 | Coriell Institute for Medical Research | HG01889 |
| GM02752 | Coriell Institute for Medical Research | GM02752 |
| GM20805 | Coriell Institute for Medical Research | GM20805 |
| Software and algorithms | ||
| Bedtools (v2.31.1) | Aaron R. Quinlan et al. | https://bedtools.readthedocs.io/en/latest/ |
| BWA-MEM (v0.7.17) | Heng Li et al. | https://github.com/lh3/bwa |
| compleasm (v0.2.7) | Neng Huang et al. | https://github.com/huangnengCSU/compleasm |
| GenomeScope (v2.0) | Rhyker Ranallo-Benavidez et al. | https://github.com/schatzlab/genomescope |
| IGV (v2.18.2) | Robinson et al. | https://igv.org/ |
| mashmap (v3.1.1) | Chirag Jain et al. | https://github.com/marbl/MashMap |
| merqury (v1.4.1) | Arang Rhie et al. | https://github.com/marbl/merqury |
| meryl (v1.4.1) | Arang Rhie et al. | https://github.com/marbl/merqury |
| Minimap2 (v2.30) | Heng Li | https://lh3.github.io/minimap2/ |
| ModDotPlot (v0.9.0) | Sweeten et al. | https://github.com/marbl/ModDotPlot |
| paftools | Heng Li | https://lh3.github.io/minimap2/ |
| Picard (v3.3.0) | https://github.com/lh3/bwa | |
| Rustybam (v0.1.33) | Mitchell R Vollger et al. | https://www.vollgerlab.com/rustybam/ |
| Samblaster (v0.1.26) | Gregory G. Faust et al. | https://github.com/GregoryFaust/samblaster |
| Samtools (v1.21) | Heng Li et al. | https://www.htslib.org/ |
| scipy (v1.13.1) | Virtanen, P., et al. | https://scipy.org/ |
| seqtk (v1.4) | Heng Li | https://github.com/lh3/seqtk |
| statsmodels (v0.14.5) | Seabold and Skipper et al. | https://www.statsmodels.org/stable/index.html |
| Verkko (v2.2.1) | Dmitry Antipov et al. | https://github.com/marbl/verkko |
| Yak (yak-0.1 (r56)) | Heng Li | https://github.com/lh3/yak |