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 trialInteractive, 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
CUT&RUN and CUT&TAG
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 priced...you CAN get all three!! Thank you to the folks at Basepair for helping us deal with some difficult RNA Seq data."
"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."
"Support answers come fast and are always precise!"
