Table 1 Benchmark datasets

HG002 Pacbio CCS 15kb+20 kb

Hifi_L1

56.3×

https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/PacBio_CCS_15kb_20 kb_chemistry2/reads/

HG002 PacBio CCS 10 kb

Hifi_L2

30×

https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/PacBio_CCS_10 kb/

HG002 PacBio CCS 11kb

Hifi_L3

34×

https://www.ncbi.nlm.nih.gov/sra/SRR8833180

HG002 PacBio CCS 15kb

Hifi_L4

28×

https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/PacBio_CCS_15kb/

HG002 PacBio CCS 16kb

Hifi_L5

41×

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA832505

HG002 MtSinai

CLR_L1

65.1×

https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/PacBio_MtSinai_NIST/

HG002 Pacbio CLR

CLR_L2

88.6×

https://www.ncbi.nlm.nih.gov/sra/SRX7668835

HG002 Pacbio CLR

CLR_L3

28.6×

https://www.ncbi.nlm.nih.gov/sra/SRX6719924

HG002 Nanopore Promethion

Nano_L1

45.6×

https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/UCSC_Ultralong_OxfordNanopore_Promethion/

HG002 Nanopore UL guppy3.2.4

Nano_L2

57×

ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/Ultralong_OxfordNanopore/guppy-V3.2.4_2020-01-22/

HG002 Nanopore PRJNA678534

Nano_L3

48×

https://www.ncbi.nlm.nih.gov/Traces/study/?acc = SRP292617&o = acc_s%3Aa

9 Simulated long reads datasets

Hifi_TRA Hifi_DUP Hifi_INV CLR_TRA CLR_DUP CLR_INV ONT_TRA ONT_DUP ONT_INV

40×

CLR&ONT: VISOR+PBSIM3; Hifi: VISOR+PBSIM3+CCS

HCC1395 Tumor Pacbio

HCC1395_PB

39×

https://www.ncbi.nlm.nih.gov/sra/?term = SRR8955953

HCC1395 Normal Pacbio

HCC1395BL_PB

44×

https://www.ncbi.nlm.nih.gov/sra/?term = SRR8955954

HCC1395 Tumor ONT

HCC1395_ONT

12×

https://www.ncbi.nlm.nih.gov/sra/?term = SRR16005301

HCC1395 Normal ONT

HCC1395BL_ONT

19×

https://www.ncbi.nlm.nih.gov/sra/?term = SRR17096031