Pinned Repositories
ContainedReadRemoval
CoverageNormalization
Scripts for normalizing coverage in samples with highly amplified regions
Grafter
Scaffolding with Ultralong Reads
Iris
A module for improving the insertion sequences of structural variant calls
Jasmine
Jasmine: SV Merging Across Samples
sapling
SAPLING: Suffix Array Piecewise Linear INdex for Genomics
TAG2020
The course website for my Fall 2020 course "Theory and Applications of Graphs"
TelomericMSA
Unitigging
Implementation of Unitigging Algorithm from "Toward Simplifying and Accurately Formulating Fragment Assembly (Myers et. al., 1995)
vcfigv
Code for generating IGV screenshots from VCF files
mkirsche's Repositories
mkirsche/Jasmine
Jasmine: SV Merging Across Samples
mkirsche/Iris
A module for improving the insertion sequences of structural variant calls
mkirsche/sapling
SAPLING: Suffix Array Piecewise Linear INdex for Genomics
mkirsche/Grafter
Scaffolding with Ultralong Reads
mkirsche/CoverageNormalization
Scripts for normalizing coverage in samples with highly amplified regions
mkirsche/vcfigv
Code for generating IGV screenshots from VCF files
mkirsche/ContainedReadRemoval
mkirsche/TelomericMSA
mkirsche/SVMergingMethodComparison
Analyzes results of merging variants
mkirsche/TAG2020
The course website for my Fall 2020 course "Theory and Applications of Graphs"
mkirsche/VariantValidator
mkirsche/bioconda-recipes
Conda recipes for the bioconda channel.
mkirsche/canu
A single molecule sequence assembler for genomes large and small.
mkirsche/chm13plotting
mkirsche/CrossStitchEval
A collection of scripts for evaluating the performance of different pieces of CrossStitch
mkirsche/JasmineFigures
mkirsche/JasmineResults
Software for measuring and visualizing Jasmine results
mkirsche/libdivsufsort
A lightweight suffix-sorting library
mkirsche/LongReadFilter
mkirsche/mkirsche.github.io
A minimal Jekyll Theme to host your resume (CV)
mkirsche/nCovIllumina
mkirsche/react-tutorial
mkirsche/sketch
C++ Implementations of sketch data structures with SIMD Parallelism, including Python bindings
mkirsche/Sketching
Scripts related to sketching data structures
mkirsche/StrandDifferences
Highlights strand-specific differences in MAF in ONT data
mkirsche/sv-merger
Forms SV cliques using the CAST (Cluster Affinity Search Technique) algorithm.
mkirsche/SVGraph
Code for experimenting with representation of structural variants as novel adjacencies in a reference graph
mkirsche/SVMergeEval
Some scripts for evaluating the performance of SV merging software
mkirsche/svpop
Variant annotation and merging pipeline
mkirsche/SVRecall
Simple method for double checking presence of a samples' SVs in a panel