The JGI has diverse capabilities in DNA and RNA sequencing, sample and library preparation, DNA synthesis and pathway engineering, and mass spectrometry based metabolomics. Below is a list of standard sequencing products, including a description of the product and deliverables as well as target cycle times from sample receipt to completion of standard analysis.
For custom requests not on these lists, we encourage you to contact the relevant program leads to discuss available options.
| Scientific Program | Product | Brief Description | Deliverables | FY18 target cycle time (median), days | FY18 target cycle time (75th %), days |
|---|---|---|---|---|---|
| Fungal | Minimal Draft | Lower coverage whole genome shotgun sequencing. | Assembly, annotation (Mycocosm); raw data submitted to SRA | 250 | 400 |
| Fungal | Resequencing | SNP and short indel calls, rearrangement detection, population analysis. | Text file of SNPs (incl location in genome, coding/vs non, syn vs non-syn aa change etc) and structural rearrangements, alignment files and fastq files; raw data submitted to SRA | 140 | 200 |
| Fungal | Standard Draft | Whole genome shotgun sequencing. Exact scope items and quality of finished product depend on genome. Selected genomes will be improved based on feasibility and scientific merit. | Assembly, annotation (Mycocosm); raw data submitted to SRA | 250 | 400 |
| Fungal | Transcriptome | RNA for expression profiling and genome annotation | For annotation: de novo assembly. For counting: text file of gene counts (mapped against reference transcriptome or de novo assembly), alignment files and raw data. Raw data submitted to SRA. | 135 | 163 |
| Metagenome | Metatranscriptome | Environmental transcript sequence from prokaryotes and/or eukaryotes | Assembly, annotation (IMG/M), mapping to metagenome if applicable; raw data submitted to SRA | 180 | 200 |
| Metagenome | Cell Enrichments |
Obtained by physical separation of a biologically relevant unit from a microbial community, such as a microcolony, microbial aggregate, or a specific subset of free-living cells. Due to the low biomass of cell enrichments, the extracted DNA may be amplified using whole-genome amplification prior to sequencing. | Assembly, annotation (IMG/M); raw data submitted to SRA | 140 | 200 |
| Metagenome | Minimal Draft | Lower-coverage assembly & annotation of environmental DNA (note the JGI is no longer supporting iTag sequencing) | Assembly, annotation (IMG/M); raw data submitted to SRA | 140 | 200 |
| Metagenome | Standard Draft | Assembly & annotation of environmental DNA. Selected metagenomes will be improved based on feasibility and scientific merit. (Note the JGI is no longer supporting iTag sequencing) | Assembly, annotation (IMG/M); raw data submitted to SRA | 150 | 170 |
| Microbial | Improved Draft, Isolate | High Quality Draft assembly computationally analyzed and improved. Semi-manual. | Assembly, annotation (IMG), methylation analysis | 150 | 190 |
| Microbial | Minimal Draft, Isolate | Lowest quality microbial draft product, many unordered contigs. | Assembly, annotation (IMG); raw data submitted to SRA | 150 | 240 |
| Microbial | Minimal Draft, Single Cell | Lowest quality microbial draft product, many unordered contigs. | Assembly, annotation (IMG); raw data submitted to SRA | 150 | 190 |
| Microbial | Single Particle Sort | Draft assembly of whole genome amplified sorted cell(s)/particle(s) | Assembly, annotation (IMG/M); raw data submitted to SRA | 150 | 190 |
| Microbial | Resequencing | SNP and short indel calls, rearrangement detection, population analysis. | Text file of SNPs (incl location in genome, coding/vs non, syn vs non-syn aa change etc) and structural rearrangements, alignment files and fastq files; raw data submitted to SRA | 100 | 110 |
| Microbial | Transcriptome | RNA for expression profiling. | For counting: text file of gene counts (mapped against reference transcriptome), alignment files and raw data (fastq format). Raw data submitted to SRA. | 100 | 222 |
| Plant | Resequencing | SNP and short indel calls, rearrangement detection, population analysis. | Text file of SNPs (incl location in genome, coding/vs non, syn vs non-syn aa change etc) and structural rearrangements, alignment files and fastq files; raw data submitted to SRA | 140 | 200 |
| Plant | Standard Draft | Whole genome shotgun sequencing. Sequencing generated for initial evaluation varies depending on genome characteristics, availability of external resources and project goals. Selected genomes will be improved based on feasibility and scientific merit. | Assembly, annotation (Phytozome); raw data submitted to SRA | depends on genome | depends on genome |
| Plant | Transcriptome | RNA for expression profiling and genome annotation. | For annotation: de novo assembly. For counting: text file of gene counts (mapped against reference transcriptome or de novo assembly), alignment files and raw data. Raw data submitted to SRA. | 180 | 240 |