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.
GQC (Genome Quality Checker)
GQC is a benchmarking tool for evaluating sequence reads and assemblies against a genome benchmark.
TTT
Trivial Tangle Traverser (TTT) is a tool developed to construct model sequences for the remaining gaps in the T2T assemblies and replace error-prone and labour-intensive manual graph curation step.
AniAnn's
AniAnn's is a tandem repeat annotation and masking tool which can infer repeat structure across whole chromosomes without sequence alignment.
Verkko-Fillet
Post-verkko graph and assembly curation in Python
ModDotPlot
ModDotPlot is a dotplot visualization tool, built for scalability to visualizae large tandem repeats across whole chromosomes.
T2T-Polish
Evaluation and polishing workflows for T2T genome assemblies
Merfin
Evaluate variant calls and its combination with k-mer multiplicity
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