kdm9/usc-demo

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Created over 8 years ago
Updated almost 8 years ago

kdm9/usc-demo

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Demo of the userspace containers project at the Common Workflow Language

kWIP

De novo estimates of genetic relatedness from next-gen sequencing data

axe

Rapid competitive read demulitplexer. Made with tries.

SRApy

SRA python tools

hail

Hail: extract lines from a file, a la `head -n x | tail -n y`

clogged

Tiny, configurable, pretty C logging library

seqhax

Small sequence analysis tools that don't deserve their own repos.

bioscripts

A Collection of Bioinformatic Scripts

Acanthophis

A comprehensive, opinionated plant variant calling pipeline in Snakemake

NVTK

Tools for managing natural variation collections

2020_snakemake-workshop

Paneuc-acanthophis

Analysis of ~1000 eucalyputs genomes with the acanthophis pipeline

pbshax

pandoc-notes

Take notes using vim, pandoc, xetex and vim-pandoc

boringLD

2020_hpa-geogenet

texlive-local

Dummy package to allow texlive to be installed locally

onlign

Online alignment prototypes for ANU improvements to AUGUR

FastaSanitiser

A python class/cli to sanitise fasta IDs to something sane, then back again. Lookin' at you, gisaid_sequences.fasta

euc-dp15-workspace

libqcpp

libqc++: C++11 library for next-gen sequence quality control and assessment.

kdmRutil

venv.jl

Python-style virtual environments in Julia

panjournal

Pandoc templates meet journal latex templates

PaneucalyptShortReads

pyNGSQC

A pure-python next-gen sequencing quality control library, and soon to be command line tool

kmer-distance-workshop

gbstrim

Trim GBS reads of adaptors and reduce over-inflation of allele counts.

kdm-tor

My UNOFFICIAL dev branch of tor. See torproject.org for the real thing

raijin-ansible

Configure and install group-wide software modules on Raijin using ansible