UMI-based variant calling

Unique molecular identifiers (UMIs) are a type of molecular barcoding that provides error correction and increased accuracy on Next Generation Sequencing (NGS) data. UMIs allow for the identification of PCR duplicates and the correction of sequencing errors, which are common sources of false positives.

Sequencing accuracy using UMI-based reads significantly reduces false positives and increases variant calling sensitivity, allowing to confidently call variants with a frequency below 1%.

Genomic UMI-based Variant Calling Pipeline

A workflow designed to process UMI-based NGS reads for individual or multi-sample designs. Enables the detection of low frequency SNVs and INDELs, while providing genomic context through functional and database annotations.

All the steps in the pipeline are based on open source reference bioinformatics tools, considered as standards for the genomic UMI-based variant calling analysis.

  • FastQC: Quality controls of reads

  • fgbio: Process UMI-based reads

  • Picard: Manipulate high-throughput sequencing data

  • Samtools: Interact with alignment files

  • VarScan2: Perform variant calling

  • BCFtools: Operate with variant calling files

  • VEP: Perform variant annotation


The pipeline provides multiple plots and tables to explore the analyzed data.

Quality control metrics for sequence reads

Read alignment statistics

Insert size metrics

UMI read consensus

Variant calling and statistics

Variant annotation and statistics

  • Price: $35

    Average per sample

  • Runtime: 2 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 RNA-Seq 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 RNA-Seq 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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