cgroza

GraffiTE

GraffiTE is a pipeline that finds polymorphic transposable elements in genome assemblies and/or long reads, and genotypes the discovered polymorphisms in read sets using genome-graphs.

KU_tutorial_2023

personalized_genomes_gbio

pggb

the pangenome graph builder

BarcodeAsm

bifrost_jaccard

Compute jaccard similarity matrix between colors in a bifrost compacted colored de Bruijn graph.

Biomorph

Biomorph program written in Java that aims to simulate evolution by mutation and natural selection with polygons and a turn function.

dotfiles

nextflow_scripts

panmethyl

Map Pacbio methylation data to genome graphs.

SeqLib

C++ htslib/bwa-mem/fermi interface for interrogating sequence data

arxiv-latex-cleaner

arXiv LaTeX Cleaner: Easily clean the LaTeX code of your paper to submit to arXiv

Bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

cgroza.github.io

cljgfa

Clojure parser for GFA2 format.

ConvolutionDrugClassifier

Convolutional neural network drug classifer.

CrossMap

CrossMap is a python program to lift over genome coordinates from one genome version to another.

gcloud_nextflow

Nextflow pipeline for SURVIVOR.

graph_peak_caller

ChIP-seq peak caller for reads mapped to a graph-based reference genome

hifiasm_nextflow

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

NanoVar

Structural variant caller for low-depth long-read sequencing data

nearestpaths

Find nearest paths in a genome graph

pangenie_nextflow

Nextflow script to run PanGenie on thousands of samples.

repeatR

read and analyse RepeatMasker output

sane-mmtag

Program that parses base modifications data in BAM files and outputs read annotations in sane BED-like coordinates.

smoothxg

linearize and simplify variation graphs using blocked partial order alignment

sv_segway

svaba

Structural variation and indel detection by local assembly

twauctex

Tweaks for AUCtex