143 citations · 153 across the 6 of their papers we have counts for
6 papers
Computing all-vs-all MEMs in grammar-compressed text
Diego Diaz-Dominguez, Leena Salmela
We describe a compression-aware method to compute all-vs-all maximal exact matches (MEM) among strings of a repetitive collection . The key concept in our work is the…
Computing all-vs-all MEMs in run-length encoded collections of HiFi reads
Diego Díaz-Domínguez, Simon J. Puglisi, Leena Salmela
We describe an algorithm to find maximal exact matches (MEMs) among HiFi reads with homopolymer errors. The main novelty in our work is that we resort to run-length compression to…
ViQUF: de novo Viral Quasispecies reconstruction using Unitig-based Flow networks
Borja Freire, Susana Ladra, José R. Paramá +1
During viral infection, intrahost mutation and recombination can lead to significant evolution, resulting in a population of viruses that harbor multiple haplotypes. The task of re…
Extraction of long k-mers using spaced seeds
Miika Leinonen, Leena Salmela
The extraction of k-mers from sequencing reads is an important task in many bioinformatics applications, such as all DNA sequence analysis methods based on de Bruijn graphs. These…
Accurate selfcorrection of errors in long reads using de Bruijn graphs
Leena Salmela, Riku Walve, Eric Rivals +1
New long read sequencing technologies, like PacBio SMRT and Oxford NanoPore, can produce sequencing reads up to 50,000 bp long but with an error rate of at least 15%. Reducing the…
Pattern Kits
Travis Gagie, Kalle Karhu, Juha Kärkkäinen +2
Suppose we have just performed searches in a self-index for two patterns and and now we want to search for their concatenation \A B); how can we best make use of our previo…