Key resources table
| Deposited data | ||
| Strand-seq: NA19036 | This paper | NCBI: PRJEB39750 |
| Strand-seq: NA19434 | This paper | NCBI: PRJEB39750 |
| Strand-seq: HG00268 | This paper | NCBI: PRJEB39750 |
| Strand-seq: HG01352 | This paper | NCBI: PRJEB39750 |
| Strand-seq: HG01573 | This paper | NCBI: PRJEB39750 |
| Strand-seq: HG02018 | This paper | NCBI: PRJEB39750 |
| Strand-seq: HG02059 | This paper | NCBI: PRJEB39750 |
| Strand-seq: HG02106 | This paper | NCBI: PRJEB39750 |
| Strand-seq: HG04217 | This paper | NCBI: PRJEB39750 |
| Strand-seq: LCL pools | This paper | NCBI: PRJEB39750 |
| Strand-seq: trio samples (n=9) | (Chaisson et al., 2019) | NCBI: PRJEB12849 |
| Strand-seq: other samples (n=34) | (Ebert et al., 2021) | NCBI: PRJEB39750 |
| Strand-seq: HG002/NA24385 | Public HPRC data (https://github.com/human-pangenomics/HG002_Data_Freeze_v1.0) | https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=NHGRI_UCSC_panel/HG002/hpp_HG002_NA24385_son_v1/Strand_seq/ |
| Strand-seq: NA12878 | (Porubský et al., 2016) | NCBI: PRJEB14185. |
| WGS Illumina data (1KG panel) | (Byrska-Bishop et al.) | NCBI: PRJEB37677 |
| RNA-seq data | (Ebert et al., 2021) | NCBI SRA: ERP123231 |
| PacBio data 1 | (Ebert et al., 2021) | NCBI: PRJEB36100 |
| PacBio data 2 | (Ebert et al., 2021) | EBI/ENA: ERP125611 |
| PacBio data 3 | (Ebert et al., 2021) | NCBI: PRJNA698480 |
| PacBio data: HG00268 | N/A | NCBI: PRJNA558774 |
| PacBio data: HG01352 | N/A | NCBI: PRJNA339719 |
| PacBio data: HG02059 | N/A | NCBI: PRJNA339726 |
| PacBio data: HG02106 | N/A | NCBI: PRJNA480858 |
| PacBio data: HG04217 | N/A | NCBI: PRJNA481794 |
| PacBio data: NA19434 | N/A | NCBI: PRJNA385272 |
| Oxford Nanopore: HG00733 ultra-log | (Logsdon et al., 2021) | NCBI: PRJNA686388 |
| Oxford Nanopore: HG00733 | (Shafin et al., 2020) | NCBI: PRJEB37264 |
| Oxford Nanopore: NA19240 | N/A | NCBI: PRJEB26791 |
| Oxford Nanopore: HG002/NA24385 | (Shafin et al., 2020) | https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/UCSC_Ultralong_OxfordNanopore_Promethion/ |
| BioNano data | (Ebert et al., 2021) | EBI/ENA: ERP124807 |
| 1KG phased genotypes for 3,202 samples | (Byrska-Bishop et al.) | http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_phased/ |
| Phased SNVs (VCFs) and inversion genotype tables | This paper | http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC2/working/20210917_SSEQplusWHintegrativePhasing_inversionCallset/ |
| HGSVC phased assemblies (PGAS v12) | (Ebert et al., 2021) | https://www.internationalgenome.org/data-portal/data-collection/hgsvc2 |
| HGSVC phased assemblies (PGAS v13) | (Ebler et al. 2022) | DOI:10.5281/zenodo.5607680 |
| Dot plot visualizations of several recurrent inversion loci | This paper | http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC2/working/20220209_recurrent_inversions_resolved/ |
| Software and algorithms | ||
| primatR | (Porubsky et al., 2020) | https://github.com/daewoooo/primatR |
| breakpointR | (Porubsky et al., 2019) | https://github.com/daewoooo/breakpointR |
| StrandPhaseR | (Porubsky et al.,2017), New functionalities added in this paper | https://github.com/daewoooo/StrandPhaseR, branch=devel |
| ArbiGent | This paper | DOI:10.5281/zenodo.6405196 |
| PAV | (Ebert et al., 2021) | https://github.com/EichlerLab/pav |
| MEIGA-PAV | (Ebert et al., 2021), New functionalities added in this paper | DOI:10.5281/zenodo.6077336 |
| ti-SNPs detection | This paper | DOI:10.5281/zenodo.6405152 |
| Detection of altered SD organization | This paper | DOI:10.5281/zenodo.6411308 |
| Mendelian consistency analysis | This paper | DOI:10.5281/zenodo.6411714 |
| BWA aligner (v0.7.15–0.7.17) | (Li and Durbin, 2010) | http://bio-bwa.sourceforge.net/ |
| SAMtools (v1.3.1–1.10) | (Li et al., 2009) | http://samtools.sourceforge.net/ |
| sambamba (v1.0) | (Tarasov et al., 2015) | https://lomereiter.github.io/sambamba/ |
| RTG tool (v3.11) | Copyright (c) 2018 Real Time Genomics Ltd | https://www.realtimegenomics.com/products/rtg-tools |
| Relate (v1.1.7) | (Speidel et al., 2019) | https://myersgroup.github.io/relate/ |
| IQ-TREE (v2.1.3) | (Minh et al., 2020) | http://www.iqtree.org/ |
| SV-Pop | (Audano et al., 2019; Ebert et al., 2021) | https://github.com/EichlerLab/svpop |