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GitHub / kdm9 100 repositories
Hacking on DNA
kdm9/bfx-containers
Language: Dockerfile - Size: 38.1 KB - Last synced: 5 days ago - Pushed: 6 days ago - Stars: 0 - Forks: 0
kdm9/Augustus Fork of Gaius-Augustus/Augustus
Genome annotation with AUGUSTUS
Language: C++ - Size: 539 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 0 - Forks: 0
kdm9/Acanthophis
A comprehensive, opinionated plant variant calling pipeline in Snakemake
Language: TeX - Size: 587 KB - Last synced: 9 days ago - Pushed: 2 months ago - Stars: 5 - Forks: 2
kdm9/raugraf
Language: Python - Size: 28.3 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0
kdm9/seqhax
Small sequence analysis tools that don't deserve their own repos.
Language: C - Size: 2.31 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 8 - Forks: 0
kdm9/rab
Size: 104 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0
kdm9/samtools Fork of samtools/samtools
Language: C - Size: 14.4 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0
kdm9/kWIP
De novo estimates of genetic relatedness from next-gen sequencing data
Language: C++ - Size: 3.82 MB - Last synced: about 15 hours ago - Pushed: almost 5 years ago - Stars: 44 - Forks: 3
kdm9/blindschleiche
19 bioinformatics utilities in a trenchcoat
Language: Python - Size: 113 KB - Last synced: about 1 month ago - Pushed: 2 months ago - Stars: 1 - Forks: 0
kdm9/Paneuc-acanthophis
Analysis of ~1000 eucalyputs genomes with the acanthophis pipeline
Language: Jupyter Notebook - Size: 32.4 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 2 - Forks: 1
kdm9/snakemake-executor-plugin-slurm Fork of snakemake/snakemake-executor-plugin-slurm
A Snakemake executor plugin for submitting jobs to a SLURM cluster
Language: Python - Size: 49.8 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0
kdm9/snakemake Fork of snakemake/snakemake
This is the development home of the workflow management system Snakemake. For general information, see
Size: 86.9 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0
kdm9/gvcf_norm Fork of mlin/gvcf_norm
gVCF allele normalizer
Size: 10.3 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0
kdm9/trears
Language: OpenSCAD - Size: 158 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0
kdm9/borg Fork of borgbackup/borg
Deduplicating archiver with compression and authenticated encryption.
Language: Python - Size: 27.1 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0
kdm9/notebook-template
Language: CSS - Size: 127 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0
kdm9/markdown-lightbox2 Fork of stlehmann/markdown-lightbox
extension for python markdown to lightbox images
Language: CSS - Size: 45.9 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0
kdm9/SQANTI3 Fork of ConesaLab/SQANTI3
Tool for the Quality Control of Long-Read Defined Transcriptomes
Language: HTML - Size: 323 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0
kdm9/tkdm
Language: Python - Size: 15.6 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0
kdm9/libqcpp
libqc++: C++11 library for next-gen sequence quality control and assessment.
Language: C++ - Size: 2.89 MB - Last synced: 8 months ago - Pushed: about 7 years ago - Stars: 1 - Forks: 1
kdm9/2016_pip-brachy-vc
Language: Python - Size: 1.95 KB - Last synced: 8 months ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0
kdm9/euc-dp15-workspace
Language: R - Size: 27.7 MB - Last synced: 8 months ago - Pushed: over 5 years ago - Stars: 1 - Forks: 0
kdm9/NVTK
Tools for managing natural variation collections
Language: Python - Size: 378 KB - Last synced: 19 days ago - Pushed: about 2 months ago - Stars: 3 - Forks: 1
kdm9/onlign
Online alignment prototypes for ANU improvements to AUGUR
Language: Python - Size: 14.6 KB - Last synced: 10 months ago - Pushed: about 4 years ago - Stars: 1 - Forks: 0
kdm9/paco_ot2
Language: Python - Size: 263 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0
kdm9/MetaPhlAn Fork of biobakery/MetaPhlAn
MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
Size: 4.8 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0
kdm9/diamond Fork of bbuchfink/diamond
Accelerated BLAST compatible local sequence aligner.
Size: 31.4 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0
kdm9/axe
Rapid competitive read demulitplexer. Made with tries.
Language: C - Size: 1.09 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 21 - Forks: 5
kdm9/NLRtracker Fork of slt666666/NLRtracker
NLR annotation tool
Language: R - Size: 852 KB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0
kdm9/sam2lca Fork of maxibor/sam2lca
Lowest Common Ancestor from a SAM/BAM/CRAM alignment file
Size: 95.5 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0
kdm9/bcftools Fork of samtools/bcftools
This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib
Language: C - Size: 16.9 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0
kdm9/bacterial_GWAS_tutorial Fork of janepipistrelle/bacterial_GWAS_tutorial
Tutorial for bacterial GWAS pipline and bugwas, created for Bodega Bay 2016 NGS workshop
Size: 75.2 KB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0
kdm9/tnseq Fork of jbadomics/tnseq
documentation and scripts for analyzing Tn-seq data
Language: Python - Size: 23.1 MB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0
kdm9/python-rocksdb-feedstock Fork of conda-forge/python-rocksdb-feedstock
A conda-smithy repository for python-rocksdb.
Size: 43.9 KB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0
kdm9/workflows Fork of common-workflow-library/legacy
Community maintained workflows & tools (with examples)
Language: Python - Size: 3.17 MB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0
kdm9/filo Fork of arq5x/filo
Useful FILe and stream Operations
Language: C++ - Size: 56.6 KB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0
kdm9/lab-notebook
Writeups of various things
Language: Jupyter Notebook - Size: 1.7 MB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0
kdm9/bloscpack Fork of Blosc/bloscpack
Command line interface to and serialization format for Blosc
Language: Python - Size: 1.61 MB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0
kdm9/dawg Fork of CartwrightLab/dawg
Simulating Sequence Evolution
Language: C++ - Size: 3.1 MB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0
kdm9/jared_climate
Language: Python - Size: 7.81 KB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0
kdm9/BBS_Meeting_2015 Fork of biospectrabysequencing/BBS_Meeting_2015
Programme, notes, slides etc. related to BBS meeting prior to MapNet2015
Size: 69.3 KB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0
kdm9/lpipy
LPI.py: Lineage Probablity Index calculation in Python
Language: Python - Size: 168 KB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0
kdm9/stacks
My changes to Stacks, the reduced representation sequencing assembler and variant caller
Language: C++ - Size: 664 KB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 2
kdm9/2015_kwip-samplesum
Debugging the samplesum mismatches
Language: Python - Size: 3.45 MB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0
kdm9/2015_kwip-96rice-00-normalisation
Language: Python - Size: 156 KB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0
kdm9/2015_gbs-insert-sizes
Language: C++ - Size: 883 KB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 1
kdm9/Seq-Gen Fork of rambaut/Seq-Gen
Sequence simulator
Language: C - Size: 150 KB - Last synced: about 1 year ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0
kdm9/snakes
My Snakemake rules for bioinformatics
Size: 125 KB - Last synced: about 1 year ago - Pushed: almost 9 years ago - Stars: 0 - Forks: 0
kdm9/bamtools Fork of pezmaster31/bamtools
C++ API & command-line toolkit for working with BAM data
Language: C++ - Size: 3.71 MB - Last synced: about 1 year ago - Pushed: almost 9 years ago - Stars: 0 - Forks: 0
kdm9/zstd-stream
C++11 Zstd iostream subclasses
Size: 125 KB - Last synced: about 1 year ago - Pushed: almost 9 years ago - Stars: 0 - Forks: 0
kdm9/screed Fork of dib-lab/screed
a simple read-only sequence database, designed for short reads
Language: Python - Size: 767 KB - Last synced: about 1 year ago - Pushed: over 9 years ago - Stars: 0 - Forks: 0
kdm9/scikit-image Fork of scikit-image/scikit-image
Image Processing SciKit (Toolbox for SciPy)
Language: Python - Size: 33.1 MB - Last synced: about 1 year ago - Pushed: over 9 years ago - Stars: 0 - Forks: 0
kdm9/scythe Fork of vsbuffalo/scythe
A 3'-end adapter contaminant trimmer
Language: C - Size: 922 KB - Last synced: about 1 year ago - Pushed: over 9 years ago - Stars: 0 - Forks: 0
kdm9/ansible-modules-core Fork of ansible/ansible-modules-core
Ansible modules - these modules ship with ansible
Size: 5.29 MB - Last synced: about 1 year ago - Pushed: over 9 years ago - Stars: 0 - Forks: 0
kdm9/fastDBarcode
DEPRECATED: Use AXE, at
Language: C - Size: 1.05 MB - Last synced: about 1 year ago - Pushed: almost 10 years ago - Stars: 0 - Forks: 0
kdm9/hons-finalpresentation
Final presentation of my 2013 Honours project
Size: 92.7 MB - Last synced: about 1 year ago - Pushed: over 10 years ago - Stars: 0 - Forks: 1
kdm9/pyexiv2 Fork of escaped/pyexiv2
Fork, which allows installation using pip. No support. Use it as it is ;-)
Size: 398 KB - Last synced: about 1 year ago - Pushed: over 10 years ago - Stars: 0 - Forks: 0
kdm9/bcbb Fork of chapmanb/bcbb
Incubator for useful bioinformatics code, primarily in Python and R
Language: Python - Size: 10.4 MB - Last synced: about 1 year ago - Pushed: almost 11 years ago - Stars: 0 - Forks: 0
kdm9/libngs Fork of sylvainforet/libngs
The Nifty GNU Sequence Library
Language: C - Size: 497 KB - Last synced: about 1 year ago - Pushed: about 11 years ago - Stars: 1 - Forks: 0
kdm9/kCAT Fork of dutilh/CAT
CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs)
Language: Python - Size: 4.3 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
kdm9/kdm-snakemake-helpers 📦
OBSOLETE: see https://github.com/kdm9/Acanthophis
Language: Python - Size: 8.79 KB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0
kdm9/SRApy 📦
SRA python tools
Language: Python - Size: 73.2 KB - Last synced: about 14 hours ago - Pushed: almost 3 years ago - Stars: 10 - Forks: 6
kdm9/bash_kernel Fork of takluyver/bash_kernel
A bash kernel for IPython
Language: Python - Size: 70.3 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
kdm9/mkdocs-table-reader-plugin Fork of timvink/mkdocs-table-reader-plugin
MkDocs plugin that adds a {{ read_csv('table.csv') }} markdown tag to directly insert CSV files as a table into a page.
Size: 89.8 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
kdm9/stringtie Fork of gpertea/stringtie
Transcript assembly and quantification for RNA-Seq
Size: 6.51 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
kdm9/makro-stacking-rail
Language: Python - Size: 5.86 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
kdm9/gbs-snakemake 📦
Classes for GBS analysis using snakemake and stacks
Language: Python - Size: 6.84 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0
kdm9/svglue2 Fork of mbr/svglue
Create templates using Inkscape, then fill them in (and render them to PDF, if you like).
Language: Python - Size: 45.9 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
kdm9/gbstrim 📦
Trim GBS reads of adaptors and reduce over-inflation of allele counts.
Language: Python - Size: 141 KB - Last synced: about 1 year ago - Pushed: about 9 years ago - Stars: 1 - Forks: 1
kdm9/www.kdmurray.id.au 📦
My website source
Language: CSS - Size: 327 KB - Last synced: about 1 year ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0
kdm9/cyvcf2 Fork of brentp/cyvcf2
cython + htslib == fast VCF and BCF processing
Size: 14.1 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
kdm9/kmin
A minimal hugo theme. Clean, simple, minimalist.
Language: HTML - Size: 20.5 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0
kdm9/papermill Fork of nteract/papermill
📚 Parameterize, execute, and analyze notebooks
Size: 1.91 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0
kdm9/jupytext Fork of mwouts/jupytext
Jupyter Notebooks as Markdown Documents, Julia, Python or R scripts
Size: 24.6 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0
kdm9/zsh-autoactivate-conda
Language: Shell - Size: 3.91 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0
kdm9/hail
Hail: extract lines from a file, a la `head -n x | tail -n y`
Language: C - Size: 12.7 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 7 - Forks: 1
kdm9/PaneucalyptPostanalysis
Language: Python - Size: 2.18 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0
kdm9/2020_snakemake-workshop
Language: Shell - Size: 133 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 3 - Forks: 1
kdm9/pandora Fork of rmcolq/pandora
Pan-genome inference and genotyping with long noisy or short accurate reads
Size: 280 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
kdm9/gfakluge Fork of edawson/gfakluge
A C++ library and utilities for manipulating the Graphical Fragment Assembly format.
Size: 1.86 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
kdm9/bioconda-recipes Fork of bioconda/bioconda-recipes
Conda recipes for the bioconda channel.
Language: Shell - Size: 365 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0
kdm9/2020_hpa-geogenet
Language: R - Size: 229 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0
kdm9/make_prg Fork of leoisl/make_prg
Code to create a PRG from a Multiple Sequence Alignment file
Size: 2.21 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
kdm9/hugo-theme-even-less
A fork of Hugo's Even theme with some extra features I needed
Language: SCSS - Size: 644 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0
kdm9/msprime-feedstock Fork of conda-forge/msprime-feedstock
A conda-smithy repository for msprime.
Size: 121 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0
kdm9/clogged
Tiny, configurable, pretty C logging library
Language: C - Size: 101 KB - Last synced: about 1 year ago - Pushed: over 7 years ago - Stars: 6 - Forks: 0
kdm9/kwip-experiments
Language: Jupyter Notebook - Size: 27.9 MB - Last synced: about 1 year ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0
kdm9/xspin
hacks around knitr::spin() for shell and python scripts
Language: R - Size: 11.7 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
kdm9/hugo-nicer-figures
Language: HTML - Size: 6.84 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
kdm9/windowlickR
Windowed vcf analyses in R
Language: C++ - Size: 119 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
kdm9/radhax
Scripts for analysis of reduced-representation sequencing (GBS, RADseq)
Language: Python - Size: 70.3 KB - Last synced: 7 days ago - Pushed: 7 months ago - Stars: 0 - Forks: 0
kdm9/conda-pkgs
My conda packages. mamba install -c kdm801 $PGK to install
Language: Shell - Size: 71.3 KB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 0
kdm9/holy-build-box Fork of phusion/holy-build-box
System for building cross-distribution Linux binaries
Language: Shell - Size: 348 KB - Last synced: about 1 year ago - Pushed: over 7 years ago - Stars: 0 - Forks: 1
kdm9/dnglab Fork of dnglab/dnglab
Camera RAW to DNG file format converter
Size: 1.19 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0
kdm9/dna-proto-workflow Fork of warthmann/dna-proto-workflow
Snakemake ProtoWorkflow for DNA Analysis.
Size: 262 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0
kdm9/pbshax
Language: Python - Size: 12.7 KB - Last synced: 21 days ago - Pushed: almost 3 years ago - Stars: 2 - Forks: 0
kdm9/sourmash Fork of sourmash-bio/sourmash
Compute and compare MinHash signatures for DNA data sets.
Language: Standard ML - Size: 13.8 MB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0
kdm9/LEA Fork of bcm-uga/LEA
Size: 4.27 MB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0