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.
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS sequencing.
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WES sequencing.
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.
Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel.
A single-cell RNA seq pipeline for 10X genomics data using cell ranger and providing a QC report.
Spatial analysis pipelines from 10X Genomics (SpaceRanger) and BGI STOmics (StereoMap, StereoPy).
ChIP-seq peak-calling, QC and differential analysis pipeline.
A small-RNA sequencing analysis pipeline, aligning to a chosen genome and to miRbase annotated smallRNAs. Table of gene coutns provided.
ATAC-seq peak-calling and QC analysis pipeline.
Shotgun metagenomics and metagenomic-assembly genome (MAG) analysis.
Amplicon sequencing analysis workflow using DADA2 and QIIME2.
Amplicon sequencing analysis workflow using DADA2 and QIIME2.
