mkirsche

Jasmine

Jasmine: SV Merging Across Samples

Iris

A module for improving the insertion sequences of structural variant calls

sapling

SAPLING: Suffix Array Piecewise Linear INdex for Genomics

Grafter

Scaffolding with Ultralong Reads

CoverageNormalization

Scripts for normalizing coverage in samples with highly amplified regions

vcfigv

Code for generating IGV screenshots from VCF files

ContainedReadRemoval

TelomericMSA

chm13plotting

SVMergingMethodComparison

Analyzes results of merging variants

TAG2020

The course website for my Fall 2020 course "Theory and Applications of Graphs"

VariantValidator

bioconda-recipes

Conda recipes for the bioconda channel.

canu

A single molecule sequence assembler for genomes large and small.

CrossStitchEval

A collection of scripts for evaluating the performance of different pieces of CrossStitch

JasmineFigures

JasmineResults

Software for measuring and visualizing Jasmine results

libdivsufsort

A lightweight suffix-sorting library

LongReadFilter

mkirsche.github.io

A minimal Jekyll Theme to host your resume (CV)

nCovIllumina

react-tutorial

sketch

C++ Implementations of sketch data structures with SIMD Parallelism, including Python bindings

Sketching

Scripts related to sketching data structures

StrandDifferences

Highlights strand-specific differences in MAF in ONT data

sv-merger

Forms SV cliques using the CAST (Cluster Affinity Search Technique) algorithm.

SVGraph

Code for experimenting with representation of structural variants as novel adjacencies in a reference graph

SVMergeEval

Some scripts for evaluating the performance of SV merging software

svpop

Variant annotation and merging pipeline

SVRecall

Simple method for double checking presence of a samples' SVs in a panel