matt-shenton Goto Github PK

blasr

This is an unsupported fork of the PacBio blasr aligner. It contains my (very beta) optimizations and new functionality. It may disappear at any time.

blink

dbg2olc

The genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.

gridlmm

GridLMM package

hapcut2

software tools for haplotype assembly from sequence data

hgrainbow

Supplementary data and scripts used in the article "Haplotype-based genome wide association study using a novel SNP-set method : RAINBOW"

hisat2

Graph-based alignment (Hierarchical Graph FM index)

mathematical_morphology_with_morpholibj

A collection of demonstration materials for MorphoLibJ.

mindthegap

MindTheGap performs detection and assembly of DNA insertion variants in NGS read datasets with respect to a reference genome.

momi-g

Modular Multi-scale Integrated Genome Graph Browser

morpholibj

Collection of mathematical morphology methods and plugins for ImageJ

msa2gfa

A script to extract graph structure from multiple sequence alignment result and output as GFA/JSON for vg

msa_tubemap

Visualize multiple sequence alignment as variation graph on Sequence Tube Map

orientationj

ImageJ's plugin for directional analysis in images: color-coded analysis, distribution of orientation, vector field, keypoint detection

ricecorehub

sequencetubemap

displays multiple genomic sequences in the form of a tube map

silico

a simulator of long read sequencing in pacbio and oxford nanopore

sommer

variantannotation

Annotation of Genetic Variants

vg

tools for working with genome variation graphs