ammaraziz

wfi

whofluIRMA - influenza assembly pipeline

ctgap

Chlamydia trachomatis Genome Assembly Pipeline

flukit

extract_reads

Extract reads from kraken quickly and easily

nextclade_viral_datasets

A collection of custom Nextclade viral datasets for genotyping of tiny viruses

rospalloc

tutorials

a place to store tutorials

2022_sarscov2_epistasis

Estimating epistatic interactions from SARS-CoV-2 genomes

assignClades

Assign influenza HA clade from consensus fasta

haplokrak

A snakemake pipeline for classifying (kraken), de novo assemblying (haploflow) and annotating (abricate) pipeline

bioconda-recipes

Conda recipes for the bioconda channel.

bioinfo-training-philippines.github.io

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

depme

Lazy detect dependencies in workflows

GISAIDR

Programmatically interact with the GISAID database.

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

olivar-primer-pipeline

piranha

prepare.py

Create a 'file of filenames' (FOFN) of samples for pipeline input - From Bactopia

rscripts

A place to store my R scripts.

seqsender

Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories

sipe

snipit

snipit: summarise snps relative to your reference sequence

tss

video-library

wf-artic

ARTIC SARS-CoV-2 (ONT amplicon) workflow and reporting