Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Chemicals, peptides, and recombinant proteins | ||
| McCoy’s 5A Modified Medium | American Type Culture Collection (ATCC) | Cat# 30-2007 |
| ATCC-formulated RPMI- 1640 Medium | American Type Culture Collection (ATCC) | Cat# 30-2001 |
| ATCC-formulated Dulbecco’s Modified Eagle’s Medium | American Type Culture Collection (ATCC) | Cat# 30-2002 |
| Critical commercial assays | ||
| Monarch® Genomic DNA Purification Kit | New England Biolabs (NEB) | Cat# T3010S |
| Qubit™ HS dsDNA assay | ThermoFisher - Invitrogen | Cat# Q32851 and Q32854 |
| ONT Genomic DNA Ligation kit | Oxford Nanopore Technologies (ONT) | Cat# SQK-LSK109 |
| NEBNext® Companion Module for Oxford Nanopore Technolo gies® Ligation Sequencing | New England Biolabs (NEB) | Cat# E7180S |
| Agilent 4200 TapeStation (Genomic DNA ScreenTape) | Agilent | Cat# 5067-5366 |
| Nanopore R9 MinION flow cell | Oxford Nanopore Technolo gies (ONT) | Cat# FLO-MIN106D |
| NEBnext FFPE DNA Repair Mix | New England Biolabs (NEB) | Cat# M6630S |
| NEBNext Ultra II End Repair/dA tailing Module | New England Biolabs (NEB) | Cat# E7442L |
| Nanopore PromethION R9.4.1 flow cell | Oxford Nanopore Technolo gies (ONT) | Cat# FLO-PRO002 |
| PacBio SMRTbell Express Template Prep Kit 2.0 | Pacific Biosciences (PacBio) | Cat# 100-938-900 |
| SMRTbell Enzyme Clean Up Kit 2.0 | Pacific Biosciences (PacBio) | Cat# 101-938-500 |
| BluePippin™ Dye Free 0.75% Agarose Gel Cassettes | Sage Science | Cat# BHZ7510 |
| Sequel II Binding Kit 2.2 | Pacific Biosciences (PacBio) | Cat# 101-908-100 |
| Sequel IIe 8M SMRT Cells | Pacific Biosciences (PacBio) | Cat# 101-389-001 |
| Sequel II Sequencing 2.0 Kit | Pacific Biosciences (PacBio) | Cat# 101-820-200 |
| Agencourt® AMPure XP | Beckman Coulter | Cat# A63881 |
| Commercial spectral karyotyping paint probes from Applied Spectral Imaging | Applied Spectral Imaging (5315 Avenida Encinas, Suite 150, Carlsbad, CA92008) | - |
| Deposited data | ||
| Nanopore PromethION long-read sequencing datasets | This paper | To be uploaded to SRA database (pending accessision number) |
| Nanopore MinION long-read sequencing dataset | This paper | To be uploaded to SRA database (pending accessision number) |
| PacBio HiFi long-read sequencing datasets | This paper | To be uploaded to SRA database (pending accessision number) |
| Illumina short-read sequencing datasets | This paper | To be uploaded to SRA database (pending accessision number) |
| Whole genome short-read sequencing dataset from the Cancer Cell Line Encyclopedia | Ghandi et al7 | PRJNA523380 |
| Whole genome short-read sequencing dataset of lung adenocarcinoma patients from The Cancer Genome Atlas | Carrot-Zhang et al and Campbell et al70,71 | https://gdc.cancer.gov/about-data/publications/pancanatlas |
| dbSNP (build 151) | Sherry et al72 | ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/common_all_20180418.vcf.gz |
| GRCh38 reference genome | UCSC Genome Browser | https://hgdownload.soe.ucsc.edu/downloads.html |
| CHM13 reference genome | Nurk et al73 | https://github.com/marbl/CHM13 |
| Experimental models: Cell lines | ||
| U2OS cells | American Type Culture Collection (ATCC) | Cat# HTB-96™ |
| NCI-BL1184 cells | American Type Culture Collection (ATCC) | Cat# CRL-5949™ |
| NCI-H1184 cells | American Type Culture Collection (ATCC) | Cat# CRL-5858™ |
| Hs-746T cells | American Type Culture Collection (ATCC) | Cat# HTB-135 |
| Software and algorithms | ||
| TelFuse | This paper | https://github.com/ktan8/teltools/ |
| TelSize | This paper | https://github.com/ktan8/teltools/ |
| Minimap2 v2.17-r941 | Li74 | https://github.com/lh3/minimap2 |
| BWA-MEM v0.7.17-r1188 | Li75 | https://github.com/lh3/bwa |
| SAMtools v1.10 | Li et al76 | https://github.com/samtools/samtools |
| R v4.2.0 | R Foundation for Statistical Computing77 | https://www.r-project.org/ |
| Python v3.7.4 | Van Rossum et al78 | https://www.python.org/ |
| Perl v5.26.2 | Wall et al79 | http://www.perl.org/ |
| Integrative Genomics Viewer (IGV) | Thorvaldsdottir el al80 | https://software.broadinstitute.org/software/igv/ |
| Bonito v0.3.5 | Oxford Nanopore Technolo gies (ONT) | https://github.com/nanoporetech/bonito |
| Bonito basecalling model for telomeric reads | Tan et al81 | https://github.com/ktan8/nanopore_telomere_basecall |
| Other | ||
| Covaris® g-TUBE | Covaris® | Cat# 520079 |
| Megaruptor 3 system | Diagenode | B06010003 |
| PippinHT | Sage Science | Cat# HTP0001 |
| Sequel IIe instrument | Pacific Biosciences (PacBio) | - |