2 citations · 3 across the 5 of their papers we have counts for
6 papers
Towards Optimal Prefix-Free Graph Construction: NP-Hardness and Structural Insights
Andrej Baláž, Alexandru Popa
Prefix-free parsing provides an efficient way to construct compressed representations of large and repetitive pangenomes and naturally induces a graph representation known as a pre…
Wheeler maps
Andrej Baláz, Travis Gagie, Adrián Goga +4
Motivated by challenges in pangenomic read alignment, we propose a generalization of Wheeler graphs that we call Wheeler maps. A Wheeler map stores a text and an assignme…
Prefix-free graphs and suffix array construction in sublinear space
Andrej Baláž, Alessia Petescia
A recent paradigm shift in bioinformatics from a single reference genome to a pangenome brought with it several graph structures. These graph structures must implement operations,…
MARIA: Multiple-alignment -index with aggregation
Adrián Goga, Andrej Baláž, Alessia Petescia +1
There now exist compact indexes that can efficiently list all the occurrences of a pattern in a dataset consisting of thousands of genomes, or even all the occurrences of all the p…
Prefix-free parsing for building large tunnelled Wheeler graphs
Adrián Goga, Andrej Baláž
We propose a new technique for creating a space-efficient index for large repetitive text collections, such as pangenomic databases containing sequences of many individuals from th…
SnakeLines: integrated set of computational pipelines for sequencing reads
Jaroslav Budis, Werner Krampl, Marcel Kucharik +12
Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation…