Methods to build reference genomes for species where one is not available. A typical setup involves an initial draft genome assembled from long sequence reads, followed by scaffolding to get longer contigs and error-correction. This is followed by annotation of the new reference genome, eg. of genes and other functional elements.
RNA sequencing of mRNAs selected through poly-A enrichment.
library preparation transcriptomics RNA truseq mRNA illumina RNA-SeqProduction of high-quality proximity ligation libraries, using two restriction enzymes.
chromatin scaffolding library preparation epigenetics TADs illumina de novoA proximity-ligation protocol using a sequence-independent endonuclease, generating data for TAD identification and scaffolding.
chromatin scaffolding library preparation epigenetics TADs illumina de novoLow cost library preparation option for gDNA based on bead-linked transposase. Only for full plates of samples.
normalization library preparation genome illumina WGS dna nexteraGold standard method for shotgun DNA libraries used for whole genome sequencing and metagenomics.
library preparation truseq genome illumina WGS dnaLibrary preparation from limited input DNA, used in whole genome sequencing and metagenomics etc.
library preparation truseq genome illumina WGS dnaLibrary 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 dnaLoop genomics can provide both transcript counting and phasing for full length mRNA using short-reads on Illumina sequencers
library preparation RNA full length transcripts linked-reads illuminaNanopore cDNA sequencing is able to sequence entire transcripts in one go, ideal for detecting isoforms and fusions events.
assembly long-read nanoporeNanopore instruments can sequence very long continuous fragments of DNA. Sequencing native DNA allows detection of base modifications.
assembly long-read nanoporeNanopore direct RNA sequencing is able to sequence entire transcripts from native RNA, opening up opportunities to detect RNA 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 svLibrary preparation technology linking reads from long DNA fragments useful for example for de novo sequencing or phasing of variants in whole genome resequencing.
library preparation linked-reads genome illumina WGS dnaNeutronStar is a bioinformatics best-practice analysis pipeline used for de novo assembly and quality-control of 10x Genomics Chromium data. The pipeline is built using Nextflow, and comes with docker / singularity containers to make the results highly reproducible.
neutronstar de novoQuality control, Basecalling and multiplexing of sequencing reads generated by Oxford Nanopore sequencers.
long-read nanoporeAnalysis applications provided by NGI using PacBio’s open-source SMRT Analysis software suite.
assembly structural variation base modifications pacbio iso-seq ccs hifi resequencingAdditional compute intensive nanopore raw data processing services provided by NGI
methylation base modifications basecalling fast5Basic quality-control monitoring of Illumina FastQ sequence data.
QC fastqc fastq screen checkqc