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Abstract BackgroundThe pan-genome of a species is the union of the genes and non-coding sequences present in all individuals (cultivar, accessions, or strains) within that species. ResultsHere we introduce PGV, a reference-agnostic representation of the pan-genome of a species based on the notion of consensus ordering. Our experimental results demonstrate that PGV enables an intuitive, effective and interactive visualization of a pan-genome by providing a genome browser that can elucidate complex structural genomic variations. ConclusionsThe PGV software can be installed via conda or downloaded fromhttps://github.com/ucrbioinfo/PGV. The companion PGV browser athttp://pgv.cs.ucr.educan be tested using example bed tracks available from the GitHub page.
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Pangenomic genotyping with the marker array
Abstract We present a new method and software tool called that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool available athttps://github.com/alshai/rowbowt.
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- Award ID(s):
- 2029552
- PAR ID:
- 10411750
- Publisher / Repository:
- Springer Science + Business Media
- Date Published:
- Journal Name:
- Algorithms for Molecular Biology
- Volume:
- 18
- Issue:
- 1
- ISSN:
- 1748-7188
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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