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.
NEBNext EM-Seq kit is an alternative to whole-genome bisulfite sequencing (WGBS). The enzymatic conversion of unmethylated cytosines in EM-seq is more gentle to DNA than WGBS and results in libraries with more even genome coverage and better coverage of CpG sites across the genome.
WGBS EM-seq library preparation methylation epigenetics illumina CpGProduction 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-seqA proximity-ligation protocol using a sequence-independent endonuclease, generating data for TAD identification and scaffolding.
TADs illumina de novo chromatin scaffolding library preparation epigeneticsSPLAT 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 ssDNALibrary 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.
illumina WGS dna library preparation genomeNanopore instruments can sequence very long continuous fragments of DNA. Sequencing native DNA allows detection of base modifications.
long-read nanopore assemblyPacBio 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.
de novo iso seq sv smrt assembly pacbio methylation amplicon sequel hifi clrThe EPIC BeadChip array allows for the interrogation over 850,000 methylation sites quantitatively across the genome at single-nucleotide resolution.
epigenetics illumina dna array infinium CpG methylationBioinformatic 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.
base modifications pacbio assembly iso-seq structural variation ccs hifi resequencingBasic quality-control monitoring of Illumina FastQ sequence data.
QC fastqc fastq screen checkqc