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

raw sequence reads Analysis Sequence report scp MEGAHIT Anvio BEDTools Bowtie 2 Centrifuge FastQC HUMAnN2 Kraken Mash MetaQUAST MultiQC Pandas QUAST SAMtools seqtk Snakemake SPAdes SqueezeMeta numpy scikit-bio Sequence analysis

Sequence assembly Analysis Data Anvio Bowtie 2 Centrifuge SAMtools Snakemake Sequence analysis Sequence assembly

Feature table Analysis Report eukrep prodigal MEGAHIT BWA CoverM FastQC MetaBAT 2 MultiQC SAMtools Snakemake Trimmomatic CONCOCT metagenomics

Data Analysis Report BWA SAMBLASTER SAMtools Snakemake Data identity and mapping

Data Analysis Report Quant Salmon Seurat SingleCellExperiment Snakemake devtools ggplot2 Matrix rjson pybiomart Data quality management

Data index Analysis Report FastANI MMseqs NanoPlot SAMtools seqkit Snakemake Molecular evolution

Sample annotation Analysis Gene report plink2 BCFtools BEDTools ggtree GWAS Pandas pLink Quant Snakemake Variant Effect Predictor (VEP) coloc cowplot data.table dendextend dplyr ggplot2 ggrepel ggtern gridExtra kableExtra knitr metafor plyr scales showtext tidyr tidyverse numpy scipy Genetic variation preeclampsia

Sample annotation Analysis Report bracken FastQC humann kraken2 MultiQC seqkit Snakemake metagenomics

Text Analysis Report Snakemake devtools EaCoN Cell biology

Data Analysis Report MEGAHIT BWA Cutadapt SAMtools Snakemake Data quality management

JSON Data index Analysis Report Snakemake metagenomics