All Published Workflows

4 workflows that have been reviewed and published

covid-19-signal
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Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.
public

public

This is a complete standardized workflow the assembly and subsequent analysis for short-read viral sequencing. This core work...
FASTQ-illumina Query script Genome assembly Taxonomic classification tabix BCFtools BEDTools breseq BWA Consensus FastQC FreeBayes iVar kraken2 Pangolin QUAST SAMtools Snakemake vt Trim_Galore COVID19 Risk Mitigation
Free
31
phact
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This is a phylogeny workflow for batch submission to HPC cluster built with Slurm queue manager
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public

PHACT, PH ylogeny- A ware C omputation of T olerance (for amino acid substitutions), is a computational frame...
Query script Multiple sequence alignment Phylogenetic tree raxml-ng APE Bio3D Snakemake trimAl dplyr stringr ete3 Phylogeny
Free
17
ambic-epigenome
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AMBIC Epigenomics project analysis
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public

This is the git repository for AMBIC Epigenomics project with Betenbaugh and Timp lab at JHU. Use this repository for process...
Query script Methylation analysis Report macs2 sniffles tabix BCFtools BEDTools Bowtie 2 FeatureCounts Minimap2 nanopolish NGMLR Picard SAMtools Snakemake numpy pysam SURVIVOR Trim_Galore wigToBigWig epigenomics
Free
46
sparql-query-in-a-file-on-graph-database
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SPARQL query (in a file) on graph database
public

public

The demos of the FAIRness (e.g. digital resources automatically found and reused by machines) for the WP6 of the EU Horizo...
SPARQL Query script Mapping Plot SPARQL WorkflowHub Database management
Free
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