Reference-agnostic representation and visualization of pan-genomes.

ABSTRACT:

Background

The 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.

Results

Here 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.

Conclusions

The PGV software can be installed via conda or downloaded from https://github.com/ucrbioinfo/PGV . The companion PGV browser at http://pgv.cs.ucr.edu can be tested using example bed tracks available from the GitHub page.

SUBMITTER: Liang Q 

PROVIDER: S-EPMC8520301 | biostudies-literature | 2021 Oct

REPOSITORIES: biostudies-literature