Published February 15, 2024
| Version v1.1
Dataset
Open
Minichain v1.3 Benchmark Datasets
Authors/Creators
-
1.
Indian Institute of Science Bangalore
-
2.
The University of Texas at Dallas
Description
Benchmark datasets for Minichain v1.3 (https://github.com/at-cg/minichain)
These datasets accompany the manuscript "Haplotype-aware sequence alignment to pangenome graphs", G Chandra, D Gibney, and C.Jain, 2024 (under review)
File descriptions:
- MHC-CHM13.0.gfa.gz : Haplotype-aware MHC Pangenome graph constructed from 60 MHC haplotypes from HPRC, hosted at Zenodo.
- MHC_CHM13_ONT_filt.part_001.fq.gz, MHC_CHM13_ONT_filt.part_002.fq.gz : Oxford Nanopore (SRR2336508) reads from MHC region of CHM13 human genome.
- MHC_CHM13_PacBio_filt.part_001.fq.gz, MHC_CHM13_PacBio_filt.part_002.fq.gz : PacBio HiFi (SRX5633451) reads from MHC region of CHM13 human genome.
- MHC_CHM13_PacBio_filt.fq.gz : PacBio HiFi (SRR11292121) reads from MHC region of CHM13 human genome.
- Query_0.1.tar.gz, Query_1.tar.gz, Query_5.tar.gz : Simulated MHC haplotypes with 0.1%, 1% and 5% substitution rates, respectively.
Files
Files
(480.3 MB)
| Name | Size | |
|---|---|---|
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md5:96c9a32af21f741237aef8353b0e1f78
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1.5 MB | Download |
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md5:053ee198524040d59041d57a49ebc286
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76.1 MB | Download |
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md5:e0f103be2b497f05d984af2f12aca7a4
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74.6 MB | Download |
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md5:fe92bba8f586209583e264eddd0c15b8
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41.2 MB | Download |
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md5:babdda6fcb7f154c106a635b6f05205e
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40.8 MB | Download |
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md5:c61fa83c5a21796bcff3073779668c43
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40.7 MB | Download |
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md5:07eaf33606a06fa3020e84aaa2ea648b
|
67.8 MB | Download |
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md5:b0a2439bf42259a429443b9230d3260c
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68.5 MB | Download |
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md5:7e5d8628ad280be7a6633ec768bb43e5
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69.1 MB | Download |
Additional details
Software
- Repository URL
- https://github.com/at-cg/minichain
- Programming language
- C++