| Dipcall |
0.3 |
Li et al. 2018 |
DEL, INS, small indel, SNP |
https://github.com/lh3/dipcall |
| SVIM-asm |
1.0.2 |
Heller and Vingron 2021 |
DEL, INS, DUP, INV, TRA |
https://github.com/eldariont/svim-asm |
| PAV |
2.0.0 |
Ebert et al. 2021 |
DEL, INS, INV, small indel, SNP |
https://github.com/EichlerLab/pav |
| sawfish |
1.0.1 |
Saunders et al. 2025 |
INS, DEL, INV, DUP, BND |
https://github.com/PacificBiosciences/sawfish |
| FocalSV |
1.0.0 |
This paper |
DEL, INS, INV, TRA, DUP |
https://github.com/maiziezhoulab/FocalSV |
| SVIM |
1.4.2 |
Heller and Vingron 2019 |
DEL, INS, DUP, INV, TRA |
https://github.com/eldariont/svim |
| cuteSV |
1.0.11 |
Jiang et al. 2020 |
DEL, INS, DUP, INV |
https://github.com/tjiangHIT/cuteSV |
| pbsv |
2.6.2 |
|
DEL, INS, DUP, INV, TRA, CNV |
https://github.com/PacificBiosciences/pbsv |
| SKSV |
1.0.2 |
Liu et al. 2021 |
DEL, INS, DUP, INV, TRA |
https://github.com/ydLiu-HIT/SKSV |
| Sniffles2 |
2.0.6 |
Smolka et al. 2024 |
DEL, INS, DUP, INV, TRA |
https://github.com/fritzsedlazeck/Sniffles |
| Data set |
Abbreviation in the paper |
Coverage |
Source |
| HG002 PacBio CCS 15 kb+20 kb |
Hifi L1 |
56× |
https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/PacBio_CCS_15kb_20kb_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_10kb/ |
| HG002 PacBio CCS 11 kb |
Hifi L3 |
34× |
https://www.ncbi.nlm.nih.gov/sra/SRR8833180 |
| HG002 MtSinai |
CLR L1 |
65× |
https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/PacBio_MtSinai_NIST/ |
| HG002 PacBio CLR |
CLR L2 |
89× |
https://www.ncbi.nlm.nih.gov/sra/SRX7668835 |
| HG002 PacBio CLR |
CLR L3 |
29× |
https://www.ncbi.nlm.nih.gov/sra/SRX6719924 |
| HG002 Nanopore UCSC lt100 kb |
ONT L1 |
51× |
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 PRJNA678534 |
ONT L2 |
48× |
https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP292617&o=acc_s%3Aa |
| HG002 Nanopore Standard Unsheared UCSC |
ONT L3 |
47× |
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 HiFi |
HG005 HiFi |
50× |
ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/ChineseTrio/HG005_NA24631_son/PacBio_CCS_15kb_20kb_chemistry2/uBAMs/ |
| 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 |
