| Biological samples |
|
| In-house sequenced human tumor and normal samples; see Table S1
|
This study; Pleasance et al.2
|
N/A |
|
| Critical commercial assays |
|
| NEBUltra-II kit |
New England Biolabs |
Cat#E7646A |
|
| Deposited data |
|
| Long-read sequence bams |
This study |
EGA: EGAS00001001159 |
| Raw methylation data |
This study |
GEO: GSE270257
|
| Methylation normal tissue data, see Table S8
|
Bernstein et al.,81 ENCODE,82 and Loyfer et al.83
|
GEO: GSE186458
|
|
| Software and algorithms |
|
| Minimap2 (2.15) |
Li84
|
https://github.com/lh3/minimap2 |
| Ploidetect (1.3, 1.4.2) |
https://www.biorxiv.org/content/10.1101/2021.08.06.455329v1 |
https://github.com/lculibrk/Ploidetect |
| Strelka2 (2.9.10) |
Kim et al.85
|
https://github.com/Illumina/strelka |
| Mutect2 (GATK 4.2.0.0) |
https://www.biorxiv.org/content/10.1101/861054v1 |
https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2 |
| ABySS (1.3.4) |
Simpson et al.86
|
https://github.com/bcgsc/abyss |
|
Trans-ABySS (1.4.10) |
Simpson et al.,86 Birol et al.87
|
https://github.com/bcgsc/transabyss |
| Manta (1.6.0) |
Chen et al.88
|
https://github.com/Illumina/manta |
| Delly (0.8.7) |
Rausch et al.89
|
https://github.com/dellytools/delly |
| MAVIS (2.2.1; 3.1.0) |
Reisle et al.90
|
https://github.com/bcgsc/mavis |
| SNPEff (5.0) |
Cingolani et al.91
|
https://pcingola.github.io/SnpEff/ |
| BioBloomTools (2.0.11b) |
Chu et al.21
|
https://github.com/bcgsc/biobloom |
| STAR (v2.5.2b-XS and Sambamba 0.7.1; 2.7) |
Dobin et al.92
|
https://github.com/alexdobin/STAR |
| RSEM (1.3.0) |
Li & Dewey93
|
https://github.com/deweylab/RSEM |
| CIBERSORT (1.6.2) |
Newman et al.94
|
https://cibersortx.stanford.edu/ |
| SAVANA (1.0.3) |
|
https://github.com/cortes-ciriano-lab/savana |
| nanomonSV (0.5.0) |
Shiraishi et al.20
|
https://github.com/friend1ws/nanomonsv |
| CuteSV (1.0.12) |
Jiang et al.95
|
https://github.com/tjiangHIT/cuteSV |
| Sniffles (2.0.7; 1.0.12) |
Sedlazeck et al.,96 Smolka et al.97
|
https://github.com/fritzsedlazeck/Sniffles |
| RepeatMasker (4.1) |
Smit et al.98
|
https://github.com/rmhubley/RepeatMasker |
| Custom Viral Integration Workflow |
https://doi.org/10.1101/2023.11.04.564800 |
https://github.com/vanessa-porter/callONTIntegration |
| BEDTools (2.30.0, 2.23) |
Quinlan & Hall99
|
https://github.com/arq5x/bedtools2 |
| IMPALA |
https://www.biorxiv.org/content/10.1101/2023.09.11.555771v1 |
https://github.com/bcgsc/IMPALA |
| SnpSift (5.1day) |
Cingolani et al.91
|
https://github.com/pcingola/SnpSift |
| MBASED (1.34) |
Mayba et al.100
|
https://bioconductor.org/packages/release/bioc/html/MBASED.html |
| Bcftools (1.15) |
Danecek et al.101
|
https://samtools.github.io/bcftools/bcftools.html |
| MEME suite (5.4.1) |
Grant et al.102
|
https://meme-suite.org/meme/ |
| NanoMethPhase (1.2.0) |
Akbari et al.103
|
https://github.com/vahidAK/NanoMethPhase |
| DSS (2.46) |
Akbari et al.,103 Park & Wu104
|
https://www.bioconductor.org/packages/release/bioc/html/DSS.html |
| SignIT (RC1) |
|
https://github.com/eyzhao/SignIT |
| AmpliconArchitect (1.2) |
Deshpande58
|
https://github.com/virajbdeshpande/AmpliconArchitect |
| CNVkit (0.9.10.dev0) |
Talevich105
|
https://github.com/etal/cnvkit |
| CycleViz (0.1.2) |
|
https://github.com/AmpliconSuite/CycleViz |
| Circos (0.69.9) |
Krzywinski et al.106
|
https://circos.ca/ |
| IGV (2.14.1) |
Robinson et al.107
|
https://igv.org/ |
| Annotatr (1.16.0) |
Cavalcante & Sartor108
|
https://bioconductor.org/packages/release/bioc/html/annotatr.html |
| Custom plotting code in R and Python |
This study |
https://github.com/bcgsc/long_read_pog |
|
| Other |
|
| Raw and processed data |
This study |
https://www.bcgsc.ca/downloads/nanopore_pog/ |
