Fast, user-friendly NGS data analysis software for everyone

Basepair’s platform features 30+ automated NGS analysis pipelines for multiple data types, including DNA-Seq, RNA-Seq, ChIP-Seq, and ATAC-Seq. No programming required.
14-day free trial

Interactive, publication-quality NGS analysis reports

With Basepair, you don’t have to wait. Our NGS analysis software is simple, powerful, and fast thanks to a code-free UI and powerful scaling options. Choose from 30+ popular piplines that produce reports specifically designed for your data type.

DNA-Seq Data Analysis

Our DNA-Seq analysis tools include whole genome and exome analysis pipelines for QC, alignment, variant calling and annotation, indel identification, and more.


Features: Alignment, QC, Coverage, Genome Browser, Variant Browser

RNA-Seq Data Analysis

Run differential expression and pathway pipelines, generate up/down lists, align reads, trim adapters and perform other popular RNA-Seq data analyses with a click of a button.

Features: Alignment, QC, Read Counts, Expression Counts, Genome Browser

ChIP-Seq Data Analysis

ChIP-Seq analysis pipelines include alignment, motif analysis, peak calling, and more. Reports feature gene body and transcription start site heatmaps, QC plots and read counts.

Features: QC, Read Counts, Gene Bodies, Transcription Start Site, Genome Browser

scRNA-Seq Data Analysis

Basepair provides state-of-the-art tools and pipelines to extract meaningful biological insights from your scRNASeq data, without the need for extensive bioinformatics expertise or computational resources.

Features: Quality control, data normalization, dimensionality reduction, clustering, differential gene expression analysis


ATAC-Seq Data Analysis

Run our ATAC-Seq data analysis pipeline, with features like QC, alignment, and open chromatin region analysis. Generate reports with insert size, peak distribution plots, and heatmaps.


Features: Alignment, QC, Coverage, Genome Browser, Variant Browser




Our analysis pipelines include quality control, read trimming, filtering and alignment using Bowtie2, peak calling using SEACR or Homer, and differential analysis using MACS2. We also provide data visualization tools to help you explore and interpret the results of your CUT&TAG and CUT&RUN experimental data.

Features: Quality control, read trimming & filtering, alignment, peak calling, differential analysis.

Try Basepair free for 14 days

Upload and analyze up to six samples free with our 14-day trial. Choose among 30 meticulously-tested pipelines, or explore our interactive sample reports. See why some of the world’s top institutions, labs, and pharma teams are using Basepair to save thousands of hours (and dollars) for their NGS data analysis needs.

Basepair Work is in Dozens of Peer-Reviewed Journals

"Fast, excellent and reasonably CAN get all three!! Thank you to the folks at Basepair for helping us deal with some difficult RNA Seq data."

Sharen Mckay

Yale University

"I really like how easy the website is to use. And how quickly the results are generated, including figures. I would have never thought about doing a new analysis like I just did."

Emilie Montenont

NYU Langone Health

"Support answers come fast and are always precise!"


Maria Hollnagel

Ulm University