Sequencing methodologies applied at JEMU

Amplicon sequencing (or targeted amplicon sequencing)

Amplicon sequencing is a sequencing technique targeting a small number of pre-selected genomic regions. It is exceptionally useful in smaller-scale projects, test phases, result validation and obtaining sequence data of long contiguous DNA fragments. Specific known fragments of the genome are amplified by PCR and then sequenced either using Sanger or high-throughput parallel sequencing (also called next-generation sequencing).

Related approaches: DNA barcoding, multilocus sequencing, DNA metabarcoding.


The whole mitochondrial genome is sequenced after purification or capture or amplification of overlapping fragments.

Similar approaches: meta-mitogenomics

Genome Skimming

Genome skimming is a simple, shallow sequencing method (by shotgun sequencing) enabling the collection of the most repeated DNA fragments of the genome (mitochondrial genomes and ribosomal DNA) and is highly suitable for processing large batches of samples.

Restriction site associated DNA sequencing (RAD-seq)

RAD-seq targets short DNA fragments (100-600bp) adjacent to restriction sites. This provides a reduced-representation of the whole genome because these DNA sequences flanking restriction sites are scattered across the genome.

Similar approaches: GBS (Genotype-By-Sequecning), ddRAD, HyRAD. HyRAD sequencing is a modification of traditional RAD sequencing, wherein a library of RAD baits is created and subsequently used to capture target RAD tags in the focal specimen. This technology is preferred over traditional RAD sequencing when processing DNA samples of low quality and/or quantity.


Whole Genome Resequencing

Whole genome resequencing provides an exhaustive screening of the entire genome thereby identifying genomic variants such as SNPs, indels and chromosomal rearrangements.


High-throughput RNA sequencing allows in-depth transcriptome profiling and a precise quantification of levels of transcripts and their isoforms.


QuantSeq focusses on exploring differential gene expression profiles between samples by sequencing only 70-100 base pairs at the 3’ end of poly(A) RNA transcripts. It’s a cost-efficient method to process a high number of samples and can also be applied to low quality DNA samples.

Scratchpads developed and conceived by (alphabetical): Ed Baker, Katherine Bouton Alice Heaton Dimitris Koureas, Laurence Livermore, Dave Roberts, Simon Rycroft, Ben Scott, Vince Smith