All Published Workflows
11 workflows that have been reviewed and published
Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
This is a complete standardized workflow the assembly and subsequent analysis for short-read viral sequencing.
This core work...
Transparent and robust SARS-CoV-2 variant calling and lineage assignment with comprehensive reporting.
A reproducible and scalable workflow for transparent and robust SARS-CoV-2
variant calling and lineage assignment with com...
JSON
raw sequence reads
Variant calling
genetic variants
delly
nanofilt
rust-bio-tools
snakemake-wrapper-utils
tabix
BCFtools
Biopython
BWA
CANU
Consensus
fastp
FastQC
fgbio
FreeBayes
GFFutils
kallisto
Kraken
Krona
Medaka
metaspades
Minimap2
MultiQC
Pandas
Pangolin
Picard
Quant
QUAST
SAMtools
Snakemake
Variant Effect Predictor (VEP)
vembrane
altair
intervaltree
numpy
pysam
requests
Varlociraptor
COVID19 Risk Mitigation
SARS cov2 consensus from variation/COVID-19 CONSTRUCTION
This workflow aims at generating reliable consensus sequences from variant calls according to transparent criteria that captu...
sars-cov-2-pe-illumina-wgs-variant-calling/COVID-19-PE-WGS-ILLUMINA
This workflows performs paired end read mapping with bwa-mem followed by
sensitive variant calling across a wide range of AFs...
COVID-19: variation analysis on WGS SE data
This workflows performs single end read mapping with bowtie2 followed by
sensitive variant calling across a wide range of AFs...
COVID-19: variation analysis on ARTIC PE data
The workflow for Illumina-sequenced ampliconic data builds on the RNASeq workflow
for paired-end data using the same steps fo...
COVID-19 Variation analysis Workflow
This workflow takes VCF datasets of variants produced by any of the
"*-variant-calling" workflows in
https://github.com/galax...
COVID-19 PubSeq Public Sequence Workflow
This repository provides a sequence uploader for the COVID-19 Virtual
Biohackathon's Public Sequence Resource project. There ...
A simulation about mask wearing in public schools in the Greater Houston Area
With increasing incidences of COVID-19 infections in the Greater Houston Area and students returning to school, informed ...
Frequency of COVID-19 testing to ensure workplace safety
In a population where there is a constant threat of community infection, there is a need to test everyone to ensure workplace...
Effect of quarantine for the control of COVID19 outbreaks
From the result of the risk of COVID-19 outbreak in an enclosed environment , it was clear that it is risky to introduce ...