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

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

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.

Our reports have been published in dozens of peer-reviewed journals

Feedback from our customers

Fast, excellent and reasonably priced...you 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