Shotgun Metagenomics Marker Based Profiling

Shotgun metagenomics provides information of the total genomic DNA from all organisms in a sample. Unlike previous techniques, shotgun metagenomics allows investigators to sequence thousands of organisms in parallel from a single sample, obtaining comprehensive information to evaluate bacterial diversity, microbial abundance and compare data from different time points and environments.

The importance of microbiomes has been underappreciated for a long time. With the aid of next-generation sequencing (NGS), the significance of metagenomics and its impact in medicine, ecology, industry and many other areas is now being revealed.

Marker Based Profiling Pipeline

A workflow that performs an end to end metagenomics analysis, including quality controls, taxonomic profiling, microbial diversity and abundance as well functional analysis to identify gene families and metabolic network activity.

This metagenomic workflow uses clade-specific marker genes for an accurate and fast microbiome and functional profiling analysis. All the steps in the pipeline are based on open source reference bioinformatics tools, considered as standards for the analysis of metagenomics data.

  • KneadData: Quality controls on metagenomic sequencing data

  • MetaPhlAn: Profile composition of microbial communities

  • Phyloseq: Analyze and graphically display phylogenetic data

  • Vegan: Analyze diversity, community ordination and dissimilarity

  • Krona: Interactive exploration of relative abundances

  • HUMAnN: Profile microbial gene families and pathways

  • Lefse: Differential abundance analysis

  • ANCOM-BC: Analysis of compositions of microbiomes

  • MaAsLin: Multivariable associations between microbiome features


All results are integrated in a single interactive report with tables and plots for each step performed by the pipeline.

Quality control metrics for sequence reads

Microbiome hierarchical abundance

Microbiome sample diversity

UniFrac distance heatmap

Sample ordination biplot

Metabolic pathway profiling

  • Price: $14

    Average per sample

  • Runtime: 7 hrs

    Average per study

Why BatchX

BatchX offers a serverless infrastructure for running bioinformatics analyses as a fully managed service. With the click of a button, off-load all your complex processing requirements to the cloud in a cost-effective, secure, and scalable way.

Take full control of your analysis

Our metagenomics pipeline gives you the flexibility to customize it to suit your needs. It's super easy to change any parameter and re-run the analysis with the click of a button.

Bioinformatics analysis made easy

Our no code environment gives you the freedom you need to run the metagenomics pipeline with zero coding required. Share your results with collaborators in a secure and private manner.

Custom support

Get instant assistance for any issue from our extended and experienced bioinformatics team through dedicated slack channels, emails, or conference calls.

Our users love us

BatchX allows us to carry out the metagenomic analyses we need quickly and efficiently. The platform’s flexibility and the availability of the team allowed us to improve and adapt the workflows to meet our needs. As a rookie in bionformatics, BatchX is a source of inspiration, showing me how far bioinformatic analyses can go.

Ignacio Montero

Bioinformatician, Microviable Therapeutics

BatchX is super easy to use. Any bioinformatician who deals with complex pipelines including 16S will appreciate the efficiency – import scripts once and never worry about recurring errors. We also enjoyed per job cost updates.

Adrian Santiago Ortiz

Bioinformatician, IMOMA

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