Ammar Aziz's repositories
nextclade_viral_datasets
A collection of custom Nextclade viral datasets for genotyping of tiny viruses
2022_sarscov2_epistasis
Estimating epistatic interactions from SARS-CoV-2 genomes
bioconda-recipes
Conda recipes for the bioconda channel.
compression_benchmark
Benchmarking fastq compression with generic (mature) compression algorithms
conda_irma_recipe
Custom conda IRMA recipe
cud
Color Universal Design colourblind-friendly python matplotlib palette
GISAIDR
Programmatically interact with the GISAID database.
jev
jev analysis pipelines for ncbi ingestion, nextclade dataset creation and phylo analysis
monkeypox-nf
A monkeypox virus (MPXV) assembly pipeline using Nextflow for host-removal, reference-based assembly, and generation of sequence quality metrics for Illumina paired-end data using a shotgun metagenomic sequencing approach.
mpx-vidrl
Monkeypox analysis workflow for ARTIC and TWIST
nf-mvp
A minimum viable Nextflow pipeline (Bioinformatics Clinic)
notfieldbioinformatics
The ARTIC field bioinformatics pipeline - a fork that tries to not suck
prepare.py
Create a 'file of filenames' (FOFN) of samples for pipeline input - From Bactopia
rscripts
A place to store my R scripts.
sc2_ont_benchmark
SC2 ONT Benchmark dataset for testing lineage calling
seqsender
Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
snipit
snipit: summarise snps relative to your reference sequence
ubinfie.github.io
µbinfie blog
wf-artic
ARTIC SARS-CoV-2 workflow and reporting