![Our Services - Data Visualisation](https://23899467.fs1.hubspotusercontent-na1.net/hub/23899467/hubfs/Our%20Services%20-%20Data%20Visualisation.jpg?width=300&name=Our%20Services%20-%20Data%20Visualisation.jpg)
Bioinformatics Pipelines
The SAGC provides a suite of analysis pipelines developed both externally and in-house, based on community best practises.
Workflows designed for SAGC sequenced libraries with set endpoints for quick turnaround.
![Whole Genome](https://23899467.fs1.hubspotusercontent-na1.net/hub/23899467/hubfs/Icon%20-%20Whole%20Genome.png?width=300&name=Icon%20-%20Whole%20Genome.png)
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS sequencing.
![Whole Exome](https://23899467.fs1.hubspotusercontent-na1.net/hub/23899467/hubfs/Icon%20-%20Whole%20Exome.png?width=300&name=Icon%20-%20Whole%20Exome.png)
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WES sequencing.
![RNAseq](https://23899467.fs1.hubspotusercontent-na1.net/hub/23899467/hubfs/Icon%20-%20Small%20RNA.png?width=300&name=Icon%20-%20Small%20RNA.png)
Analyse RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a FASTQ files as input, performs QC, trimming and alignment, and produces a gene expression matrix and extensive QC report.
![DNA Methylation WGBS](https://23899467.fs1.hubspotusercontent-na1.net/hub/23899467/hubfs/Icon%20-%20DNA%20Methylation%20WGBS.png?width=300&name=Icon%20-%20DNA%20Methylation%20WGBS.png)
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel.
![Single cell](https://23899467.fs1.hubspotusercontent-na1.net/hub/23899467/hubfs/Icon%20-%20Single%20cell.png?width=300&name=Icon%20-%20Single%20cell.png)
A single-cell RNA seq pipeline for 10X genomics data using cell ranger and providing a QC report.
![Spatial Transcriptomics](https://23899467.fs1.hubspotusercontent-na1.net/hub/23899467/hubfs/Icon%20-%20Spatial%20Transcriptomics-1.png?width=300&name=Icon%20-%20Spatial%20Transcriptomics-1.png)
Spatial analysis pipelines from 10X Genomics (SpaceRanger) and BGI STOmics (StereoMap, StereoPy).
![CHip seq](https://23899467.fs1.hubspotusercontent-na1.net/hub/23899467/hubfs/Icon%20-%20CHip.png?width=300&name=Icon%20-%20CHip.png)
ChIP-seq peak-calling, QC and differential analysis pipeline.
![Small RNA](https://23899467.fs1.hubspotusercontent-na1.net/hub/23899467/hubfs/Icon%20-%20Small%20RNA-1.png?width=300&name=Icon%20-%20Small%20RNA-1.png)
A small-RNA sequencing analysis pipeline, aligning to a chosen genome and to miRbase annotated smallRNAs. Table of gene coutns provided.
![ATAC-seq](https://23899467.fs1.hubspotusercontent-na1.net/hub/23899467/hubfs/Icon%20-%20ATAC-seq.png?width=300&name=Icon%20-%20ATAC-seq.png)
ATAC-seq peak-calling and QC analysis pipeline.
![Metagenomics](https://23899467.fs1.hubspotusercontent-na1.net/hub/23899467/hubfs/Icon%20-%20Metagenomics.png?width=300&name=Icon%20-%20Metagenomics.png)
Shotgun metagenomics and metagenomic-assembly genome (MAG) analysis.
![Microbiome](https://23899467.fs1.hubspotusercontent-na1.net/hub/23899467/hubfs/Icon%20-%20Microbiome.png?width=300&name=Icon%20-%20Microbiome.png)
Amplicon sequencing analysis workflow using DADA2 and QIIME2.
![Amplicons-1](https://23899467.fs1.hubspotusercontent-na1.net/hub/23899467/hubfs/Icon%20-%20Amplicons-1.png?width=300&name=Icon%20-%20Amplicons-1.png)
Amplicon sequencing analysis workflow using DADA2 and QIIME2.
TABLE OF CONTENTS
We are open to collaborative bioinformatics projects.
Contact us to schedule a free project consultation with our dedicated team of bioinformaticians.