Projects with Adam Phillippy, PhD

Senior Investigator

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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

MetAMOS

A metagenomic and isolate assembly and analysis pipeline [ retired ]

Celera Assembler PBcR

PacBio read correction and assembly pipeline [ retired ]

Krona

Interactively explore metagenomes and more from a web browser

PanArray

Pan-genome tiling array design for rapid comparative genomics

AMOSvalidate

Automated genome assembly validation [ retired ]

Insignia

DNA signature discovery for microbial detection and diagnostics [ retired ]

Hawkeye

Visual analytics for genome assembly [ retired ]

AMOScmp

Comparative genome assembler [ retired ]

AMOS

A modular sequence assembly infrastructure [ retired ]

MUMmer

Ultra-fast alignment of large-scale DNA and protein sequences