This code system https://demis.rki.de/fhir/igs/CodeSystem/sequencingStrategy defines the following codes:
| Code | Display |
| wgs | Whole Genome Sequencing - random sequencing of the whole genome (see pubmed 10731132 for details) | |
| wga | Whole Genome Amplification followed by random sequencing. (see pubmed 1631067,8962113 for details) | |
| wxs | Random sequencing of exonic regions selected from the genome. (see pubmed 20111037 for details) | |
| rna-seq | Random sequencing of whole transcriptome, also known as Whole Transcriptome Shotgun Sequencing, or WTSS). (see pubmed 18611170 for details) | |
| ssrna-seq | Strand-specific RNA sequencing. | |
| mirna-seq | Micro RNA sequencing strategy designed to capture post-transcriptional RNA elements and include non-coding functional elements. (see pubmed 21787409 for details) | |
| ncrna-seq | Capture of other non-coding RNA types, including post-translation modification types such as snRNA (small nuclear RNA) or snoRNA (small nucleolar RNA), or expression regulation types such as siRNA (small interfering RNA) or piRNA/piwi/RNA (piwi-interacting RNA). | |
| fl-cdna | Full-length sequencing of cDNA templates | |
| est | Single pass sequencing of cDNA templates | |
| hi-c | Chromosome Conformation Capture technique where a biotin-labeled nucleotide is incorporated at the ligation junction, enabling selective purification of chimeric DNA ligation junctions followed by deep sequencing. | |
| atac-seq | Assay for Transposase-Accessible Chromatin (ATAC) strategy is used to study genome-wide chromatin accessibility. alternative method to DNase-seq that uses an engineered Tn5 transposase to cleave DNA and to integrate primer DNA sequences into the cleaved genomic DNA. | |
| wcs | Random sequencing of a whole chromosome or other replicon isolated from a genome. | |
| rad-seq | RAD sequencing | |
| clone | Genomic clone based (hierarchical) sequencing. | |
| poolclone | Shotgun of pooled clones (usually BACs and Fosmids). | |
| amplicon | Sequencing of overlapping or distinct PCR or RT-PCR products. For example, metagenomic community profiling using SSU rRNA. | |
| cloneend | Clone end (5’, 3’, or both) sequencing. | |
| finishing | Sequencing intended to finish (close) gaps in existing coverage. | |
| chip-seq | ChIP-seq, Chromatin ImmunoPrecipitation, reveals binding sites of specific proteins, typically transcription factors (TFs) using antibodies to extract DNA fragments bound to the target protein. | |
| mnase-seq | Identifies well-positioned nucleosomes. uses Micrococcal Nuclease (MNase) is an endo-exonuclease that processively digests DNA until an obstruction, such as a nucleosome, is reached. | |
| dnase-hypersensitivity | Sequencing of hypersensitive sites, or segments of open chromatin that are more readily cleaved by DNaseI. | |
| bisulfite-seq | MethylC-seq. Sequencing following treatment of DNA with bisulfite to convert cytosine residues to uracil depending on methylation status. | |
| cts | Concatenated Tag Sequencing | |
| mre-seq | Methylation-Sensitive Restriction Enzyme Sequencing. | |
| medip-seq | Methylated DNA Immunoprecipitation Sequencing. | |
| mbd-seq | Methyl CpG Binding Domain Sequencing. | |
| tn-seq | Quantitatively determine fitness of bacterial genes based on how many times a purposely seeded transposon gets inserted into each gene of a colony after some time. | |
| validation | CGHub special request | |
| faire-seq | Formaldehyde Assisted Isolation of Regulatory Elements. Reveals regions of open chromatin. | |
| selex | Systematic Evolution of Ligands by Exponential enrichment | |
| rip-seq | Direct sequencing of RNA immunoprecipitates (includes CLIP-Seq, HITS-CLIP and PAR-CLIP). | |
| chia-pet | Direct sequencing of proximity-ligated chromatin immunoprecipitates. | |
| synthetic-long-read | binning and barcoding of large DNA fragments to facilitate assembly of the fragment | |
| targeted-capture | Enrichment of a targeted subset of loci. | |
| tethered-chromatin-conformation-capture | Tethered Chromatin Conformation Capture | |
| other | Library strategy not listed. | |