Cactus: a reference-free whole-genome multiple alignment program
Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described here: https://doi.org/10.1101/gr.123356.111 Cactus uses substantial reso...1721 days ago
Shouji: a fast and efficient pre-alignment filter for sequence alignment
...ncing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures....kably reduces the need for computationally-costly dynamic programming algorithms. The first key idea of our pr...1636 days ago
The wavefront alignment (WFA) algorithm
...at takes advantage ofhomologous regions between the sequences to accelerate the alignment process. As opposed to traditional dynamic programming algorithms that run in quadratic time, t...1399 days ago
1389 days ago
A guide to machine learning for biologists
...machine learning techniques, including the most recently created and frequently used deep neural network techniques. We illustrate how different algorithms may be adapted to specific ty...852 days ago
odgi: optimized dynamic genome/graph implementation
odgi provides an efficient and succinct dynamic DNA sequence graph model, as well as a host of algorithms that allow the use of such graphs in bioinformatic analyses. Careful enco...816 days ago
386 days ago