anwarmz Goto Github PK

nf-ncov-voc

A Nextflow workflow for generating the mutation profiles of SARS-CoV-2 genomes from Variants of Concern and Variants of Interest. COVID-MVP (https://github.com/cidgoh/COVID-MVP) can be used to visualize the mutations and functional annotations.

nf-seqqc

QC workflow for short-reads (Illumina) and long-reads (Oxford Nanopore) sequencing data including WGS, Amplicon and Metagenomics

nf-upcoast-v

Nextflow based WGS workflow for Vp (Will be updated later)

nf-upcoastv

nf-upcoastv-singularity

Singularity container for nf-upcoast-v (https://github.com/anwarMZ/nf-upcoast-v)

planets

pokay

Report salient qPCR primer/probe or immune epitope mismatches info against a set of pathogen isolate genomes

problematicsites_sars-cov2

python-novice-inflammation

Software Carpentry introduction to Python for novices using inflammation data.

rnaseq-nf

A proof of concept of RNAseq pipeline

rt_analysis

This repository contains script used in Anwar et al. (In preparation) for the analysis of RT data

sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

shovill

⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads

sra-download

teaching-swc-lessons

Lesson materials I have used when teaching Software Carpentry

upcoast-v

UPCOAST-V project

viralrecon

Assembly and intrahost/low-frequency variant calling for viral samples

workshop-template

Rendering of the workshop-template site