All Published Workflows

3 workflows that have been reviewed and published

strainsifter
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A straightforward bioinformatic pipeline for detecting a bacterial strain in one or more metagenome(s).
public

public

A straightforward bioinformatic pipeline for detecting the presence of a bacterial strain in one or more metagenome(s). Strai...
bacterial Phylogenetic analysis Phylogenetic tree fasttree BamTools BEDTools BWA Consensus ggtree SAMtools Snakemake ggplot2 phangorn metagenomics
Free
22
phylogenomics_intro_vertebrata
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Phylogenomics tutorial based on BUSCO genes
public

public

Phylogenomics tutorial based on BUSCO genes Disclaimer To follow the demo and make the most of it, it helps if you ha...
Genome index Phylogenetic analysis Phylogenetic tree augustus clustalo raxml-ng Biopython BUSCO IQ-TREE MAFFT API (EBI) Pandas Snakemake trimAl Whole genome sequencing
Free
55
phyloplace
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best-practice analysis pipeline that performs phylogenetic placement with EPA-NG.
public

public

nf-core/phyloplace is a bioinformatics best-practice analysis pipeline that performs phylogenetic placement with EPA-NG. T...
FASTQ raw sequence reads Phylogenetic analysis genetic variants GAPPA hmmalign (genouest) hmmbuild (genouest) MAFFT API (EBI) MultiQC Nextflow epang Phylogenetics
Free
12