Projects in Awesome Lists by kdm9
A curated list of projects in awesome lists by kdm9 .
https://github.com/kdm9/kwip
De novo estimates of genetic relatedness from next-gen sequencing data
Last synced: 03 Jan 2025
https://github.com/kdm9/axe
Rapid competitive read demulitplexer. Made with tries.
Last synced: 03 Jan 2025
https://github.com/kdm9/acanthophis
A comprehensive, opinionated plant metagenomics and variant calling pipeline in Snakemake
Last synced: 09 Apr 2025
https://github.com/kdm9/hail
Hail: extract lines from a file, a la `head -n x | tail -n y`
Last synced: 03 Jan 2025
https://github.com/kdm9/seqhax
Small sequence analysis tools that don't deserve their own repos.
Last synced: 03 Jan 2025
https://github.com/kdm9/clogged
Tiny, configurable, pretty C logging library
Last synced: 03 Jan 2025
https://github.com/kdm9/nvtk
Tools for managing natural variation collections
Last synced: 03 Jan 2025
https://github.com/kdm9/blindschleiche
31 bioinformatics utilities in a trenchcoat
Last synced: 03 Jan 2025
https://github.com/kdm9/paneuc-acanthophis
Analysis of ~1000 eucalyputs genomes with the acanthophis pipeline
Last synced: 09 Apr 2025
https://github.com/kdm9/pandoc-notes
Take notes using vim, pandoc, xetex and vim-pandoc
Last synced: 09 Apr 2025
https://github.com/kdm9/usc-demo
Demo of the userspace containers project at the Common Workflow Language
Last synced: 09 Apr 2025
https://github.com/kdm9/snakemake_executor_plugin_mpcdf
snakemake_executor_plugin_mpcdf
Last synced: 25 Feb 2025
https://github.com/kdm9/panjournal
Pandoc templates meet journal latex templates
Last synced: 09 Apr 2025
https://github.com/kdm9/fastasanitiser
A python class/cli to sanitise fasta IDs to something sane, then back again. Lookin' at you, gisaid_sequences.fasta
Last synced: 09 Apr 2025
https://github.com/kdm9/libqcpp
libqc++: C++11 library for next-gen sequence quality control and assessment.
Last synced: 09 Apr 2025
https://github.com/kdm9/raijin-ansible
Configure and install group-wide software modules on Raijin using ansible
Last synced: 09 Apr 2025
https://github.com/kdm9/onlign
Online alignment prototypes for ANU improvements to AUGUR
Last synced: 09 Apr 2025
https://github.com/kdm9/pyngsqc
A pure-python next-gen sequencing quality control library, and soon to be command line tool
Last synced: 09 Apr 2025
https://github.com/kdm9/kdm-tor
My UNOFFICIAL dev branch of tor. See torproject.org for the real thing
Last synced: 09 Apr 2025
https://github.com/kdm9/texlive-local
Dummy package to allow texlive to be installed locally
Last synced: 09 Apr 2025
https://github.com/kdm9/staticbuilder
A docker image equipt to build static binaries
Last synced: 09 Apr 2025
https://github.com/kdm9/hugo-theme-even-less
A fork of Hugo's Even theme with some extra features I needed
Last synced: 09 Apr 2025
https://github.com/kdm9/biopipes
Python module to make writing Ipython analysis workflows easier
Last synced: 09 Apr 2025
https://github.com/kdm9/ringbauer-ibd
fork of https://git.ist.ac.at/harald.ringbauer/IBD-Analysis
Last synced: 09 Apr 2025
https://github.com/kdm9/gbsqc
Demo Genotyping-by-Sequencing qc pipeline (KM version)
Last synced: 09 Apr 2025
https://github.com/kdm9/conda-pkgs
My conda packages. mamba install -c kdm801 $PGK to install
Last synced: 09 Apr 2025
https://github.com/kdm9/pipedream
Useful stuff for building distributed pipelines and data workflows
Last synced: 09 Apr 2025
https://github.com/kdm9/lpipy
LPI.py: Lineage Probablity Index calculation in Python
Last synced: 09 Apr 2025
https://github.com/kdm9/zsh-autopaths
Automatically set up $*PATH environment variables from given prefixes
Last synced: 09 Apr 2025
https://github.com/kdm9/countmin.jl
Count-min Sketch implementation for Julia
Last synced: 09 Apr 2025
https://github.com/kdm9/compressionstreams.jl
Trivial wrappers around BufferedInputStreams for transparent compression
Last synced: 09 Apr 2025
https://github.com/kdm9/gbsman
GBSman manages the analysis and storage of reduced representation sequencing.
Last synced: 09 Apr 2025
https://github.com/kdm9/libkdm
Header-only C Library which makes life easier
Last synced: 09 Apr 2025
https://github.com/kdm9/degradomeanalyser
A post-processing analysis toolkit for integrative degradomics
Last synced: 09 Apr 2025
https://github.com/kdm9/teaching-virtual-machine
Ansible code to spin up a VM for teaching bioinformatics
Last synced: 09 Apr 2025
https://github.com/kdm9/population-resequencing-simulation
A pipeline to simulate a series of populations, and then simulate reads from a resequencing experiment of each population.
Last synced: 09 Apr 2025
https://github.com/kdm9/macro-diffuser
A diffuser for the YN24-EX macro flash
Last synced: 09 Apr 2025
https://github.com/kdm9/scythe-debian
Debian package for Vince Buffalo's Scythe
Last synced: 09 Apr 2025
https://github.com/kdm9/debian-cluster-setup
Documentation and scripts for a full Debian-based Bioinformatics cluster
Last synced: 09 Apr 2025
https://github.com/kdm9/timecourse-sample-recorder
Records exact sampling times
Last synced: 09 Apr 2025
https://github.com/kdm9/birdnet-labeller
Generates an Audacity label file via ebird's Birdnet
audacity bioacoustics field-recording
Last synced: 09 Apr 2025
https://github.com/kdm9/hons-thesis
Honours thesis for Kevin Murray's 2013 honours project.
Last synced: 09 Apr 2025
https://github.com/kdm9/pete_pare_demux
Rescue index read from a PARE run whose indexing failed.
Last synced: 09 Apr 2025
https://github.com/kdm9/biofuzz
Broken files in various bioinformatic formats with which one can fuzz test parsers
Last synced: 09 Apr 2025
https://github.com/kdm9/knives
A pipelined quality control script that utilises the UC Davis Biocore's sabre, sickle, scythe and seqqs.
Last synced: 09 Apr 2025
https://github.com/kdm9/stacks
My changes to Stacks, the reduced representation sequencing assembler and variant caller
Last synced: 09 Apr 2025
https://github.com/kdm9/templates
Template and example files used in other projects, e.g. Makefiles, .gitignores etc
Last synced: 09 Apr 2025
https://github.com/kdm9/superpipes
An improved version of stdlib's `pipes` module
Last synced: 09 Apr 2025
https://github.com/kdm9/constructhelpers
Assorted helpers for G. Bradburd's conStruct
Last synced: 09 Apr 2025
https://github.com/kdm9/dcstream
(de)-compression streams for C. Supports zlib, bz2, zstd
Last synced: 09 Apr 2025
https://github.com/kdm9/multiparthandler
Updated version of MultipartPostHandler
Last synced: 09 Apr 2025
https://github.com/kdm9/axe-experiments
Experiments showing the utility of Axe
Last synced: 09 Apr 2025
https://github.com/kdm9/pymusicorganiser
pymo organises your music based on media tags
Last synced: 09 Apr 2025