Sequencing data analysis
Genomics analysis for research laboratories.
Bulk and single-cell sequencing, analysed reproducibly on HPC and delivered as results a laboratory can defend in review.
What we analyse
Five assay families, on cells or nuclei, from counts through differential testing to the figures and tables that go into a manuscript.
Bulk RNA-seq
Quantification, differential expression, pathway export.
Bulk ATAC-seq
Peak-level differential accessibility and motif enrichment.
Single-cell RNA
Per-cell-type differential expression from Seurat objects, whole cell or nuclei.
Single-nuclei ATAC
Stratified accessibility, motif and co-occurrence analysis.
Multiome
Paired RNA and ATAC from one object, extracted once and analysed together.
Variant calling
Exome and whole-genome variant discovery and annotation.
How the work is done
- Everything runs on a cluster, and everything resumes. Analyses are checkpointed stage by stage, so a failure costs the failed stage rather than the run.
- The statistics are reported, not just applied. Effect size, minimum detectable effect and power accompany the results, at the replication unit the test actually used.
- Results are traceable to the command that made them. Every output records the version, the contrast and the samples that went into each arm.
Software
The analysis framework developed here is released as open source.
Paralome
A reproducible, checkpointed workflow framework for omics analysis on HPC — one stage-graph and SLURM backbone under independent RNA, ATAC and variant pipelines.
Read about Paralome →Contact
Ken Jones
Ken.Jones@bioinformaticsolutions.com