Types of analyses supported at Sheffield
Below are examples of some of the analysis tools we regularly use and for which we can offer training.
We are open to supporting other analyses, following discussion - for more information, please contact Dr Deborah Dawson.
Population genetics & genomics
- GENEPOP, FSTAT, ARLEQUIN – genetic differentiation & diversity analyses.
- STRUCTURE, STRUCTURE HARVESTER, CLUMPP, DISTRUCT – estimating and visualising genetic clusters.
- SPAGEDI, TESS – spatial patterns of genetic diversity.
- MIGRATE – quantify past gene flow.
- MSVAR – calculating the size and timing of changes in population size.
For large data sets, such as high numbers of SNPs, genome re-sequencing or ddRAD projects:
- PLINK, POPGENOME – population genetics summary stats and basic analyses.
- STACKS, POPOOLATION – genotyping SNPs from ddRAD experiments.
- SAMTOOLS, VCFTOOLS – editing & filtering SNP files.
- BAYESCAN – detecting outlier loci.
- GENABEL – for genome-wide association studies.
- fastSTRUCTURE, DISTRUCT, NGSadmix, PCA using adegenet, fineRADstructure, RADpainter – estimating and visualising genetic clusters.
Relatedness, parentage & pedigree analyses
- ML-RELATE, RELATED – to estimate pairwise relatedness values.
- CERVUS, COLONY – parentage/sibship analysis, paternity assignment.
- MASTERBAYES – pedigree reconstruction, parentage analysis.
Metabarcoding to identify species (eg for diet analysis, eDNA & parasite detection)
We support metabarcoding for a range of applications such as diet analysis, biodiversity assessment from environmental DNA, parasite detection and MHC typing.
The follow software convert Illumina MiSeq raw sequence data to taxonomic/genotype output:
- TRIMMOMATIC, FASTQC, FLASH – assess quality, trim and align sequences.
- USEARCH, MOTHUR, QIIME, BLAST, MEGAN – cluster and categorise sequences.
- ACACIA, AmpliSAT, jMHC – genotype MHC loci.
- BEAST, MRBAYES – inferring phylogenies.
The NERC Environmental Omics Facility (NEOF)
Making state-of-the-art molecular genetics facilities and training available to the UK science community.