matt-shenton's repositories
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.
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
sequenceTubeMap
displays multiple genomic sequences in the form of a tube map
SiLiCO
a simulator of long read sequencing in pacbio and oxford nanopore
VariantAnnotation
Annotation of Genetic Variants
vg
tools for working with genome variation graphs