Single-End Antibody SEQuencing pipeline (abbreviated as SEAseq) is a comprehensive automated pipeline for ChIP-Seq/CUT&RUN data analysis. Speaking broadly, it containerizes and joins field-standard, open-source tools for processing raw data and performing a wide array of basic analyses.
SEAseq analyses include alignment, peak calling, motif analysis, read coverage profiling, clustered peak (e.g. super-enhancer) identification, and quality assessment metrics, as well as automatic interfacing with data in GEO/SRA. The easy-to-use and flexibility of SEAseq makes it a reliable and efficient resource for ensuring high quality ChIP-Seq analysis, especially in research environments lacking computational infrastructure or expertise.
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What's new in Version 3.0
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PEAseq pipeline.
PEAseq (Paired-End Antibody Sequencing Pipeline) performs all analysis provided in SEAseq and also in a paired-end aware manner; results from SEAseq will be stored under
/single-end_mode. -
A new color-rank scheme for the Quality Metrics and Evaluation Report HTML.
SEAseq pipeline requires the Cromwell jar runner, Docker or Singularity, Java (v1.8.0) and about 30GB of supplemental data.
View /test folder for example usage.
NOTE : HPC platforms using Singularity will require a configuration file to properly execute cromwell. Please consult hpc-configurations for more details.
St. Jude Users please consult SEAseq on St. Jude HPC
Before you can run SEAseq on St. Jude Cloud, you must first create a workspace in DNAnexus for the run. Refer to the general workflow guide to learn how to create a DNAnexus workspace for each workflow run.
You can navigate to the SEAseq workflow page here.
Adetunji, M.O., Abraham, B.J. SEAseq: a portable and cloud-based chromatin occupancy analysis suite. BMC Bioinformatics 23, 77 (2022). https://doi.org/10.1186/s12859-022-04588-z