ModDotPlot
ModDotPlot is a dotplot visualization tool, built to quickly visualize large complex repeats within whole chromosomes.
Verkko
Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of long accurate (e.g. PacBio HiFi) and ultra-long (e.g. Oxford Nanopore UL) reads. Verkko is Finnish for net, mesh and graph.
Merqury
Evaluate genome assemblies with k-mers and more
Winnowmap
A long-read mapping algorithm optimized for mapping ONT and PacBio reads to repetitive reference sequences.
MetaMaps
Long-read metagenomic analysis
SALSA
A tool to scaffold long read assemblies with Hi-C data
HLA*PRG:LA
Fast and efficient HLA typing from whole-genome sequencing data
MashMap
A fast and approximate long read mapper
Canu
A single molecule sequence assembler for genomes large and small
Mash
Fast genome and metagenome distance and containment estimation using MinHash
MHAP
A probabilistic sequence overlap algorithm
Harvest
A suite of core-genome alignment and visualization tools for quickly analyzing thousands of intraspecific microbial genomes
Krona
Interactively explore metagenomes and more from a web browser
PanArray
Pan-genome tiling array design for rapid comparative genomics
MUMmer
Ultra-fast alignment of large-scale DNA and protein sequences
Retired