This project stores the structural variant (SV) detection results generated by HitSV for HG002/3/4/5/6/7, the 1000 Genomes Project, HGSVC, and several non‑human species, including Macaca fascicularis, Mus musculus, Drosophila melanogaster, Danio rerio, Arabidopsis thaliana, and Glycine max.
GitHub repository of the tool: https://github.com/hitbc/HitSV
All variant detection was performed based on the GRCh38 reference genome (for human datasets). Algorithm alias: gcSV
All datasets are at 30× coverage. All results have been locally phased (pseudo-phased). The output includes the original contig sequences as well as small variants surrounding each SV.
The data were realigned to the GRCh38 reference genome.
Original data source: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/PacBio_CCS_15kb/alignment/HG002.Sequel.15kb.pbmm2.hs37d5.whatshap.haplotag.RTG.10x.trio.bam
HitSV variant calling results: https://github.com/hitbc/HitSV_call_results/HG002-LRS/ccs.30X.vcf.gz
Original data source: s3://ont-open-data/giab_2025.01/basecalling/sup/HG002/PAW70337/calls.sorted.bam
HitSV variant calling results: https://github.com/hitbc/HitSV_call_results/HG002-LRS/ont.30X.vcf.gz
Original data sources:
(downloaded using aws s3 cp)
| Sample | Data Source |
|---|---|
| HG002 | s3://ont-open-data/giab_2025.01/basecalling/sup/HG002/PAW70337/calls.sorted.bam |
| HG003 | s3://ont-open-data/giab_2025.01/basecalling/sup/HG003/PAY87794/calls.sorted.bam |
| HG004 | s3://ont-open-data/giab_2025.01/basecalling/sup/HG004/PAY87778/calls.sorted.bam |
| HG005 | s3://ont-open-data/giab_2025.01/basecalling/sup/HG005/PAW87816/calls.sorted.bam |
| HG006 | s3://ont-open-data/giab_2025.01/basecalling/sup/HG006/PAY77227/calls.sorted.bam |
| HG007 | s3://ont-open-data/giab_2025.01/basecalling/sup/HG007/PAY12990/calls.sorted.bam |
HitSV variant calling results: https://github.com/hitbc/HitSV_call_results/LRS-TRIO/HG00*.vcf.gz
Original data source: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/NIST_HiSeq_HG002_Homogeneity-10953946/NHGRI_Illumina300X_AJtrio_novoalign_bams/HG002.hs37d5.60x.1.bam
HitSV variant calling results: https://github.com/hitbc/HitSV_call_results/HG002/HG002-SRS/ILL_60X.vcf.gz
Original data source: https://opendata.nist.gov/pdrsrv/mds2-2336/input_fastqs/HG002.novaseq.pcr-free.35x.R1.fastq.gz
HitSV variant calling results: https://github.com/hitbc/HitSV_call_results/HG002/HG002-SRS/ILL_35X.vcf.gz
Original data sources: See the sections above.
HitSV variant calling results (ONT + Illumina hybrid and CCS + Illumina hybrid, respectively): https://github.com/hitbc/HitSV_call_results/HG002/HG002-Hybrid/HG002*.vcf.gz
The HGSVC (Human Genome Structural Variation Consortium) dataset contains long-read sequencing data for five individuals (HG00096, HG00268, HG00358, HG00512, HG00731). All variant calling was performed based on the GRCh38 reference genome. All datasets are at 30× coverage and results have been locally phased.
| Data Type | Data Source |
|---|---|
| PacBio HiFi reads | https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections//HGSVC3/working/20250307_Alignments_HiFi_T2T/ |
| Nanopore long reads | https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections//HGSVC3/working/20240816_JAX_ONT_guppy6_Rebasecalled/ |
HitSV LRS variant calling results (HiFi and ONT, respectively): https://github.com/hitbc/HitSV_call_results/HGSVC/HGSVC-LRS/*_HiFi30X_asm5.vcf.gz https://github.com/hitbc/HitSV_call_results/HGSVC/HGSVC-LRS/*_ONT30X_asm5.vcf.gz
HitSV was applied to several non‑human species datasets across different sequencing platforms (LRS only, SRS only, and hybrid) to demonstrate cross-species applicability. The species included are: Arabidopsis thaliana, Danio rerio, Drosophila melanogaster, Macaca fascicularis, and Mus musculus.
The following table summarizes the reference genomes, T2T assemblies, and sequencing reads used for each species:
| Species | Reference Genome | T2T Assembly | Sequencing Reads |
|---|---|---|---|
| Macaca fascicularis (Crab-eating macaque) | GCA_011100615.1 | GCF_037993035.2 | PacBio HiFi / Nanopore / Illumina — BioProject 1037719 |
| Mus musculus (Mouse) | GCF_000001635.27 | mhaESC_genome v1.1.0 | PacBio HiFi / Nanopore / Illumina — SAMN40876533 |
| Drosophila melanogaster (Fruit fly) | GCF_000001215.4 | PRJNA1237537 | PacBio HiFi / Nanopore / DNBSEQ — BioProject 1237537 |
| Danio rerio (Zebrafish) | GCF_049306965.1 | GCA_052040795.1 | PacBio HiFi / Nanopore — BioProject 1299309 |
| Arabidopsis thaliana (Thale cress) | GCF_000001735.4 | 32 ecotypes pan-genome | Nanopore: ERR11436642 · PacBio HiFi: CRR591671 · Illumina: ERR11436063 |
HitSV variant calling results (HiFi and ONT, respectively, for each species): https://github.com/hitbc/HitSV_call_results/Multi_species/*-LRS/*_HiFi_asm10.vcf.gz
HitSV variant calling results: https://github.com/hitbc/HitSV_call_results/Multi_species/*-SRS/*_SRS_asm10.vcf.gz
HitSV variant calling results (HiFi + Illumina hybrid and ONT + Illumina hybrid, respectively, for each species): https://github.com/hitbc/HitSV_call_results/Multi_species/*-Hybrid/*_HiFi4X_SRS30X_asm10.vcf.gz https://github.com/hitbc/HitSV_call_results/Multi_species/*-Hybrid/*_ONT4X_SRS30X_asm10.vcf.gz
Original data source: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/data/
Variant calling results (results from 10 randomly selected samples are provided): https://github.com/hitbc/HitSV_call_results/HG002-Hybrid/HYBRID_ILL.30X.ccs.4X.vcf.gz https://github.com/hitbc/HitSV_call_results/tree/main/1KGP-single%20sample/*.vcf.gz
Original data source: Same as above.
Variant calling results (stored separately by chromosome): https://github.com/hitbc/HitSV_call_results/blob/main/1KGP_3202_samples_gcSV_v1.0_grch38_SURVIVOR_merge/1KGP_3202_samples_gcSV_v1.0_grch38_SURVIVOR_merge_sort_chr*.vcf.gz