kdm9

Postdoctoral Fellow in Plant-pathogen Evolutionary Genomics.

Max Planck Institut für Entwicklungsbiologie, TübingenTübingen, DE

Pinned Repositories

Acanthophis
A comprehensive, opinionated plant variant calling pipeline in Snakemake
Language:TeX5 1 162
axe
Rapid competitive read demulitplexer. Made with tries.
Language:C22 4 155
blindschleiche
19 bioinformatics utilities in a trenchcoat
Language:Python1 1 00
clogged
Tiny, configurable, pretty C logging library
Language:C6 1 00
hail
Hail: extract lines from a file, a la `head -n x | tail -n y`
Language:C8 2 01
kWIP
De novo estimates of genetic relatedness from next-gen sequencing data
Language:C++44 10 263
NVTK
Tools for managing natural variation collections
Language:Python3 1 01
seqhax
Small sequence analysis tools that don't deserve their own repos.
Language:C8 1 10
SRApy
SRA python tools
Language:Python10 3 06
bash_kernel
A bash kernel for IPython
Language:Python681 27 109142

kdm9's Repositories

kdm9/axe
Rapid competitive read demulitplexer. Made with tries.
Language:C22 4 155
kdm9/seqhax
Small sequence analysis tools that don't deserve their own repos.
Language:C8 1 10
kdm9/Acanthophis
A comprehensive, opinionated plant variant calling pipeline in Snakemake
Language:TeX5 1 162
kdm9/NVTK
Tools for managing natural variation collections
Language:Python3 1 01
kdm9/blindschleiche
19 bioinformatics utilities in a trenchcoat
Language:Python1 1 00
kdm9/Augustus
Genome annotation with AUGUSTUS
Language:C++0 0
kdm9/bash_kernel
A bash kernel for IPython
Language:Python0 0
kdm9/bfx-containers
Language:Dockerfile
kdm9/bioconda-recipes
Conda recipes for the bioconda channel.
Language:Shell0 0
kdm9/borg
Deduplicating archiver with compression and authenticated encryption.
Language:Python0 0
kdm9/conda-pkgs
My conda packages. mamba install -c kdm801 $PGK to install
Language:Shell1 0
kdm9/gvcf_norm
gVCF allele normalizer
kdm9/kdm9.R
kdm9/markdown-lightbox2
extension for python markdown to lightbox images
Language:CSS0 0
kdm9/miniprothint
Miniprothint selects a set of reliable gene prediction hints from miniprot alignments scored by miniprot boundary scorer.
Language:Python0 0
kdm9/notebook-template
Language:CSS
kdm9/odgi
Optimized Dynamic Genome/Graph Implementation: understanding pangenome graphs
Language:C++0 0
kdm9/paco_ot2
Language:Python1 0
kdm9/pggb
the pangenome graph builder
Language:Shell0 0
kdm9/plassembler
Program to quickly and accurately assemble plasmids in hybrid sequenced bacterial isolates
Language:Python0 0
kdm9/rab
1 0
kdm9/radhax
Scripts for analysis of reduced-representation sequencing (GBS, RADseq)
Language:Python2 0
kdm9/raugraf
Language:Python
kdm9/samtools
Language:C1 0
kdm9/snakemake
This is the development home of the workflow management system Snakemake. For general information, see
Language:Python0 0
kdm9/snakemake-executor-plugin-slurm
A Snakemake executor plugin for submitting jobs to a SLURM cluster
Language:Python
kdm9/SQANTI3
Tool for the Quality Control of Long-Read Defined Transcriptomes
Language:HTML0 0
kdm9/tkdm
Language:Python1 0
kdm9/trears
Language:OpenSCAD
kdm9/yak
Yet another k-mer analyzer
Language:C0 0