Simka and SimkaMin are comparative metagenomics method dedicated to NGS datasets
Simka is a de novo comparative metagenomics tool. Simka represents each dataset as a k-mer spectrum and compute several classical ecological distances between them. Developper: ...1774 days ago
Cactus: a reference-free whole-genome multiple alignment program
...1 Cactus uses substantial resources. For primate-sized genomes (3 gigabases each), you should expect Cactus to use approximately 120 CPU-days of compute per genome, with about 120 GB...1737 days ago
Shouji: a fast and efficient pre-alignment filter for sequence alignment
The ability to generate massive amounts of sequencing data continues to overwhelm the processing capacity of existing algorithms and compute infrastructures. In this work, we explore...1653 days ago
RePS: Repeat-masked Phrap with scaffolding, a WGS sequence assembler
...explicitly identifies exact kmer repeats from the shotgun data and removes them prior to the assembly. The established software Phrap is used to compute meaningful error probabilitie...1592 days ago
odgi: optimized dynamic genome/graph implementation
...algorithms that allow the use of such graphs in bioinformatic analyses. Careful encoding of graph entities allows odgi to efficiently compute and transform pangenomes...832 days ago
pipesnake: bioinformatics best-practice analysis pipeline for phylogenomic reconstruction
...ing from short-read 'second-generation' sequencing data. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very por...83 days ago