Beyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References

DJ Taylor, JM Eizenga, Q Li, A Das… - Annual Review of …, 2024 - annualreviews.org
The Human Genome Project was an enormous accomplishment, providing a foundation for
countless explorations into the genetics and genomics of the human species. Yet for many …

Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes

CS Chin, S Behera, A Khalak, FJ Sedlazeck… - Nature …, 2023 - nature.com
Advancements in sequencing technologies and assembly methods enable the regular
production of high-quality genome assemblies characterizing complex regions. However …

euka: Robust tetrapodic and arthropodic taxa detection from modern and ancient environmental DNA using pangenomic reference graphs

NA Vogel, JD Rubin, M Swartz… - Methods in Ecology …, 2023 - Wiley Online Library
Ancient environmental DNA (aeDNA) is a crucial source of information for past
environmental reconstruction. However, the computational analysis of aeDNA involves the …

Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression

K Břinda, L Lima, S Pignotti, N Quinones-Olvera… - bioRxiv, 2023 - biorxiv.org
Comprehensive collections approaching millions of sequenced genomes have become
central information sources in the life sciences. However, the rapid growth of these …

AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data

JM Silva, W Qi, AJ Pinho, D Pratas - GigaScience, 2023 - academic.oup.com
Background Low-complexity data analysis is the area that addresses the search and
quantification of regions in sequences of elements that contain low-complexity or repetitive …

Compressive Pangenomics Using Mutation-Annotated Networks

S Walia, H Motwani, K Smith, R Corbett-Detig… - bioRxiv, 2024 - biorxiv.org
Pangenomics is an emerging field that uses a collection of genomes of a species instead of
a single reference genome to overcome reference bias and study the within-species genetic …

euka: Robust detection of eukaryotic taxa from modern and ancient environmental DNA using pangenomic reference graphs

NA Vogel, JD Rubin, M Swartz, J Vlieghe, PW Sackett… - bioRxiv, 2023 - biorxiv.org
Ancient environmental DNA (eDNA) is a crucial source of in-formation for past
environmental reconstruction. However, the com-putational analysis of ancient eDNA …

[PDF][PDF] A sorting tool for improving FASTA data compression tools

T Fonseca, MJP Sousa, AJ Pinho, D Pratas - eurasip.org
The exponential growth in genomic data sequenced has led to a greater need for efficient
methods to reduce data volume without loss of information. Data compression emerges as a …