All Published Workflows

3 workflows that have been reviewed and published

kizuchi
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A `snakemake` workflow for building gene trees
public

public

A snakemake workflow for phylogenomic analysis of genome clusters. kizuchi is a snakemake workflow for buildi...
Alignment Gene prediction Phylogenetic tree clustalo hmmer hmmer2 prodigal-gv Clustal Omega Clustal Omega (EBI) FastANI HMMER3 HMMER hmmscan (EBI) HMMER phmmer (EBI) hmmsearch (genouest) Snakemake Genomics
Free
10
vdblab-shotgun
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Shotgun metagenomic sequencing processing pipeline
public

public

Snakemake Apptainer/Singularity : while in many cases we do provide conda envs the only method of execution we...
Gene ID Gene prediction Gene report ABRicate AMRFinderPlus antismash-lite bracken hmmer antiSMASH BBMap Bowtie 2 cloudSPAdes CoverM dbCAN2 FastQC humann kraken2 Krona MetaErg MetaPhlAn MetaQUAST metaspades MetaWRAP plasmidspades QUAST rnaspades SAMtools seqkit Snakemake SortMeRNA SPAdes RGI Metagenomic sequencing
Free
3
metagenomic-gems-from-assembly
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Integrated Workflow: Metagenomic Bins to Metabolic Models (GEMs)
public

public

Prodigal gene prediction CarveMe genome scale metabolic model reconstruction MEMOTE for metabolic model testing ...
CWL Gene prediction eukrep prodigal BBMap BUSCO CheckM DAS fastp FastQC Filtlong Flye kraken2 Krona Medaka memote MetaBAT 2 Minimap2 n50 calculator NanoPlot SAMtools SqueezeMeta carve gtdbtk smetana Metagenomic sequencing
Free
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