Table 1.

Resource for different tools and long-read data sets

ToolsVersionResourceVariant typesLink
Dipcall0.3Li et al. 2018DEL, INS, small indel, SNPhttps://github.com/lh3/dipcall
SVIM-asm1.0.2Heller and Vingron 2021DEL, INS, DUP, INV, TRAhttps://github.com/eldariont/svim-asm
PAV2.0.0Ebert et al. 2021DEL, INS, INV, small indel, SNPhttps://github.com/EichlerLab/pav
sawfish1.0.1Saunders et al. 2025INS, DEL, INV, DUP, BNDhttps://github.com/PacificBiosciences/sawfish
FocalSV1.0.0This paperDEL, INS, INV, TRA, DUPhttps://github.com/maiziezhoulab/FocalSV
SVIM1.4.2Heller and Vingron 2019DEL, INS, DUP, INV, TRAhttps://github.com/eldariont/svim
cuteSV1.0.11Jiang et al. 2020DEL, INS, DUP, INVhttps://github.com/tjiangHIT/cuteSV
pbsv2.6.2DEL, INS, DUP, INV, TRA, CNVhttps://github.com/PacificBiosciences/pbsv
SKSV1.0.2Liu et al. 2021DEL, INS, DUP, INV, TRAhttps://github.com/ydLiu-HIT/SKSV
Sniffles22.0.6Smolka et al. 2024DEL, INS, DUP, INV, TRAhttps://github.com/fritzsedlazeck/Sniffles
Data setAbbreviation in the paperCoverageSource
HG002 PacBio CCS 15 kb+20 kbHifi L156×https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/PacBio_CCS_15kb_20kb_chemistry2/reads/
HG002 PacBio CCS 10 kbHifi L230×https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/PacBio_CCS_10kb/
HG002 PacBio CCS 11 kbHifi L334×https://www.ncbi.nlm.nih.gov/sra/SRR8833180
HG002 MtSinaiCLR L165×https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/PacBio_MtSinai_NIST/
HG002 PacBio CLRCLR L289×https://www.ncbi.nlm.nih.gov/sra/SRX7668835
HG002 PacBio CLRCLR L329×https://www.ncbi.nlm.nih.gov/sra/SRX6719924
HG002 Nanopore UCSC lt100 kbONT L151×https://s3-us-west-2.amazonaws.com/human-pangenomics/NHGRI_UCSC_panel/HG002/hpp_HG002_NA24385_son_v1/nanopore/downsampled/greater_than_100kb/HG002_ucsc_ONT_lt100kb.fastq.gz
HG002 Nanopore PRJNA678534ONT L248×https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP292617&o=acc_s%3Aa
HG002 Nanopore Standard Unsheared UCSCONT L347×https://s3-us-west-2.amazonaws.com/human-pangenomics/NHGRI_UCSC_panel/HG002/hpp_HG002_NA24385_son_v1/nanopore/downsampled/standard_unsheared/HG002_ucsc_Jan_2019_Guppy_3.4.4.fastq.gz
HG005 HiFiHG005 HiFi50×ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/ChineseTrio/HG005_NA24631_son/PacBio_CCS_15kb_20kb_chemistry2/uBAMs/
HCC1395 Tumor PacBioHCC1395 PB39×https://www.ncbi.nlm.nih.gov/sra/?term=SRR8955953
HCC1395 Normal PacBioHCC1395BL PB44×https://www.ncbi.nlm.nih.gov/sra/?term=SRR8955954
HCC1395 Tumor ONTHCC1395 ONT12×https://www.ncbi.nlm.nih.gov/sra/?term=SRR16005301
HCC1395 Normal ONTHCC1395BL ONT19×https://www.ncbi.nlm.nih.gov/sra/?term=SRR17096031

[i] Top panel: The SV calling tools used in this paper. Tool version number, cited article, variant types called by each tool, and tool links are shown in the table. Bottom panel: The long-read data sets used in this paper. The abbreviation, coverage, and source link for each data set are shown in the table. The abbreviation is used to refer to each data set in the main text.