kvg
Computational scientist working at the Broad Institute on long read methods development.
Broad InstituteCambridge, MA
Pinned Repositories
long-read-pipelines
Long read production pipelines
longbow
Annotation and segmentation of MAS-seq data
bri
Bam Read Index - Extract alignments from a bam file by readname
aou-lr
Analysis workflows for AoU long reads
badges
:pencil: Markdown code for lots of small badges :ribbon: :pushpin: (shields.io, forthebadge.com etc) :sunglasses:. Contributions are welcome! Please add yours!
cortex_tools_benchmark
For benchmarking cortexpy and cortexjdk
mccortex
Cortex on steroids: for larger populations with better assembly
MosaicAligner
Gil's HMM-based alignment/recombination software from Zilversmit et al. 2013.
notebooks
A Python notebook playground
Corticall
Germline DNM caller based on LdBG assembly of pathogens
kvg's Repositories
kvg/MosaicAligner
Gil's HMM-based alignment/recombination software from Zilversmit et al. 2013.
kvg/notebooks
A Python notebook playground
kvg/aou-lr
Analysis workflows for AoU long reads
kvg/badges
:pencil: Markdown code for lots of small badges :ribbon: :pushpin: (shields.io, forthebadge.com etc) :sunglasses:. Contributions are welcome! Please add yours!
kvg/cortex_tools_benchmark
For benchmarking cortexpy and cortexjdk
kvg/CtDNATools
Official code repository for GATK versions 4 and up
kvg/dmpy
DistributedMake for Python
kvg/mccortex
Cortex on steroids: for larger populations with better assembly
kvg/DM
DistributedMake - a perl library for pipelining with GNU make
kvg/kvg.github.io
kvg/NovelExonFinder
Uses CortexJDK to find novel exons in a transcriptome graph
kvg/PacBio
Assessments of PacBio datasets
kvg/PedanticCoalescentBook
A coalescent textbook with much more detailed derivations than usually found in treatments of coalescent theory.
kvg/pytorch-examples
Playing with PyTorch
kvg/pytorch-rust-study
kvg/readsim
Simulate DNA sequencing reads using real reads
kvg/Repro
Repro: a tool for setting up a reproducible analysis directory
kvg/sequence_gan
Generative adversarial networks (GAN) applied to sequential data via recurrent neural networks (RNN).
kvg/StatisticalRethinking
Solutions to McElreath's Statistical Rethinking textbook
kvg/Writing
Repository of writing (dissertation, articles, literature reviews, etc.)