Methods to characterise genetic or transcriptomic differences other than the nucleotide composition, e.g. 3D conformation of chromatin or levels of methylation and other DNA/RNA base modifications.
Production of high-quality proximity ligation libraries, using two restriction enzymes.
chromatin scaffolding library preparation epigenetics TADs illumina de novoA method to identify open chromatin regions, such as promotor areas, using a transposase.
ATAC open chromatin epigenetics illumina ATACseq ATAC-seqProfiling of cellular chromatin from individual cell nuclei.
ATAC open chromatin library preparation epigenetics single cell illumina ATAC-seq chromium 10x GenomicsA proximity-ligation protocol using a sequence-independent endonuclease, generating data for TAD identification and scaffolding.
chromatin scaffolding library preparation epigenetics TADs illumina de novoSPLAT is an in-house developed WGBS library preparation method. This approach enables quick and efficient preparation of WGBS libraries from low-input DNA
library preparation methylation epigenetics illumina CpG WGBS Bisulphite single-stranded DNA ssDNAA cost‐effective alternative to WGBS, by interrogating mainly the CpG-enriched fraction of the genome.
library preparation methylation epigenetics illumina CpG RRBS BisulphiteLibrary preparation for DNA, ideal for preparing libraries from small amounts of input material. Works well for shotgun libraries, ChIP DNA and FFPE samples, amongst others.
library preparation genome illumina WGS dnaNanopore instruments can sequence very long continuous fragments of DNA. Sequencing native DNA allows detection of base modifications.
assembly long-read nanoporePacBio SMRT sequencing generates reads tens of kilobases in length enabling high quality genome assembly, structural variant analysis, amplicon resequencing, full-length transcript isoform sequencing, full-length 16S rRNA sequencing and amplification free epigenetic characterization.
assembly methylation smrt pacbio amplicon sequel hifi clr de novo iso seq svThe EPIC BeadChip array allows for the interrogation over 850,000 methylation sites quantitatively across the genome at single-nucleotide resolution.
methylation epigenetics illumina dna array infinium CpGBioinformatic analysis pipeline for ATAC-seq data
chromatin open chromatin ATACseq ATAC-seqRuns with Bisulfite sequencing data. It pre-processes raw data from FastQ inputs, aligns the reads and performs extensive quality-control on the results, using either Bismark or bwa-meth/MethylDackel.
methylseq Methyl-Seq BS BisulfiteRuns with ChIP sequencing data. Pre-processes raw data from FastQ inputs, aligns the reads and performs peak calling and extensive quality-control on the results.
chipseq ChIP-SeqAnalysis applications provided by NGI using PacBio’s open-source SMRT Analysis software suite.
assembly structural variation base modifications pacbio iso-seq ccs hifi resequencingBasic quality-control monitoring of Illumina FastQ sequence data.
QC fastqc fastq screen checkqc