Ammar Aziz's repositories
extract_reads
Extract reads from kraken quickly and easily
haplokrak
A snakemake pipeline for classifying (kraken), de novo assemblying (haploflow) and annotating (abricate) pipeline
assignClades
Assign influenza HA clade from consensus fasta
fuzee
Interface to Fuzee API
nomeeting
https://sbmueller.github.io/nohello/ Website on chat etiquette. Copied from nohello.com.
assembly-stats
Assembly statistic visualisation
if-im-gone
A cheat sheet for if I am somehow incapacitated.
augur
Pipeline components for real-time phylodynamic analysis
auspice
Web app for visualizing pathogen evolution
seasonal-flu
Scripts. config, and snakefiles for seasonal-flu nextstrain builds
yml2vcf
Simple script to convert yml phe-genomics/variant_definitions to vcf
Mixture-Detection-GATK4
Variant Calling Pipeline for Haploid Mixture Analysis
MetaPhlan_pipeline
custom metaphlan pipeline for PBS schedular
phylopandas
Pandas DataFrames for phylogenetics
bash_functions
Functions I keep in my .bash files. Usually written badly by myself (to handle only very specific cases) or also possibly stolen off the internetz
bash-arg-parse
Simple CLI argument parsing template for a stand alone bash script
Multiple-sequence-alignment-Shannon-s-entropy
Parse multiple sequence alignment out put files and calculate Shannon's entropy for each column of the alignment