Repository to host the project for "Bioinformatics", a course @ FER
-
Updated
Feb 3, 2020 - C++
Repository to host the project for "Bioinformatics", a course @ FER
Evaluation tools for "A performant bridge between fixed-size and variable-size seeding"
Code to create polar sets for genome sketching.
BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Described by Firtina et al. (published in NARGAB https://doi.org/10.1093/nargab/lqad004)
GateSeeder is the first near-memory CPU-FPGA co-design for alleviating both the compute-bound and memory-bound bottlenecks in short and long-read mapping. GateSeeder outperforms Minimap2 by up to 40.3×, 4.8×, and 2.3× when mapping real ONT, HiFi, and Illumina reads, respectively.
ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
A collection of minimizer-based sampling algorithms.
Minimizer-based assembly scaffolding and mapping using long reads
Add a description, image, and links to the minimizers topic page so that developers can more easily learn about it.
To associate your repository with the minimizers topic, visit your repo's landing page and select "manage topics."