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 (d.a.dawson@sheffield.ac.uk).

    

Data validation & marker assessment

CERVUS - estimate null allele frequencies.

GENEPOP - check for Hardy-Weinberg equilibrium.

PEDANT – assess genotyping error rates.

    

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.

    

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 categorize sequences.

jMHC – genotype MHC loci.

    

Phylogenetics

BEAST, MRBAYES – inferring phylogenies.