Product Offerings
| Scientific Program | Product | Brief Description | Deliverables | Est. Amount of Material Needed | FY11 Median Cycle Time | Notes* |
|---|---|---|---|---|---|---|
| Fungal | Minimal Draft | Low coverage whole genome shotgun sequencing for evaluation. May turn into a standard draft or improved standard draft. | Assembly. Annotation optional (JGI portal); raw data submitted to SRA | 5 ug gDNA | #1 | |
| 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, tracks for upload to genome browser and fastq files; raw data submitted to SRA | 5 ug gDNA | 85 days | |
| 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 (JGI Portal + Genbank); raw data submitted to SRA | 72 ug gDNA | 230 days | |
| 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 (bam format) for upload to genome browser and raw data (fastq format). Raw data submitted to SRA. | 25 ug total RNA | 150 days | |
| Metagenome | Metatranscriptome | Environmental transcript sequence. | Assembly, annotation (IMG/M-ER), mapping to metagenome if applicable; raw data submitted to SRA | 5-25 ug total RNA | 179 days | |
| Metagenome | Pyrotags | 16/18S rRNA pyrotag sequencing | Pyrotag analysis: sff, fasta and qual files, barcode mappings, clusters and blast hits | 10 ng | 106 days | |
| Metagenome | Quick Draft | Assembly & annotation of environmental DNA | Assembly, annotation (IMG/M-ER); raw data submitted to SRA | 5 ug DNA | #1 | |
| Metagenome | Standard Draft | Assembly & annotation of environmental DNA. Selected metagenomes will be improved based on feasibility and scientific merit | Assembly, annotation (IMG/M-ER); raw data submitted to SRA | 5 ug DNA | 140 days | |
| Microbial | Improved High Quality Draft | High Quality Draft assembly computationally analyzed and improved. Semi manual. | Assembly, annotation (IMG + Genbank); raw data submitted to SRA | 50 ug gDNA | 461 days | #3 |
| Microbial | Quick Draft | Lowest quality product, many unordered contigs, short cycle time. | Assembly, annotation (IMG + Genbank); raw data submitted to SRA | 5 ug gDNA | #1 | |
| 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, tracks for upload to genome browser and fastq files; raw data submitted to SRA | 5 ug gDNA | 68 days | |
| Microbial | 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 (bam format) for upload to genome browser and raw data (fastq format). Raw data submitted to SRA. | 25 ug total RNA | 80 days | |
| Microbial | Finished | Highest quality complete genome | Assembly, annotation (IMG + Genbank); raw data submitted to SRA | 60 ug gDNA | 522 days | |
| 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, tracks for upload to genome browser and fastq files; raw data submitted to SRA | 5 ug gDNA | 123 days | |
| 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 + Genbank); raw data submitted to SRA | 200+ ug gDNA | #2 | |
| 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 (bam format) for upload to genome browser and raw data (fastq format). Raw data submitted to SRA. | 25 ug total RNA | 121 days |
* NOTES:
#1: New Product offering FY12. Cycle time expected to be less than Draft Product
#2: Cycle time dependent on genome size and complexity
#3: Cycle Time expected to be reduced in FY12
