All Published Workflows

CSV Database metadata Analysis Feature table clustalo fasttree CLICK MAFFT API (EBI) Pandas QIIME2.0 Snakemake matplotlib numpy seaborn tabulate Metagenomic sequencing

Sample annotation Sequencing quality control Quality control report OmnipathR Snakemake UniProt.ws Matrix optparse Metagenomic sequencing

FASTQ Sample annotation Variant calling genetic variants gatk Bowtie 2 FreeBayes Picard SAMtools Snakemake Trimmomatic Metagenomic sequencing

tabix Bowtie 2 CoverM fastp FastQC kraken2 MultiQC RiboDetector SAMtools Snakemake STAR Metagenomic sequencing

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

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

CWL eukrep prodigal BUSCO CheckM DAS memote MetaBAT 2 n50 calculator SqueezeMeta carve gtdbtk smetana Metagenomic sequencing

Sequence annotation turbocor MEGAHIT Bowtie 2 Flye FOCUS Kraken kraken2 MetaBAT 2 SAMtools seqtk SUPER-FOCUS TaxonKit CONCOCT singlem Metagenomic sequencing metagenomics