# iCredits
iCredits are used to purchase data storage and analysis within the Illumina cloud software ecosystem. One iCredit is equal to one US dollar (USD). iCredit balance and usage can be viewed in the [Usage Explorer](https://help.connected.illumina.com/account-management/usage-explorer). All estimates were done in AWS US East (N. Virginia) region. Storage costs can be reduced using [Archival Storage](https://help.connected.illumina.com/basespace/manage-data/archival-storage) as needed.
### :bars-progress: Default Workflows
Default workflows are out-of-the-box workflows included in Connected Multiomics Basic access. They include QC and dimension reduction features and are available for Illumina assays.
Default: Illumina Proteomics
| Assay | iCredits Per Sample | Total iCredits |
| ------------------------------------------ | ------------------- | -------------- |
| Illumina Protein Prep 9.5K with 96 samples | 0.01 | 0.96 |
Default: Illumina Single Cell Transcriptomics
Compute needs vary based on number of cells and reads obtained. Estimates below are for default analyses created for each sample in the study.
| Assay | iCredits Per Sample | Total iCredits |
| -------------------------------------------------------------------------------------------------------------- | ------------------- | -------------- |
| Illumina Single Cell 3’ RNA Prep T100 kit with 2 sample that has 318,910 cells and 40,371 features and 2.19 GB | 2.6 | 5.3 |
| Illumina Single Cell 3’ RNA Prep T20 kit with 4 samples with 99,570 cells, 40,563 features, and 587.7 MB | 0.4 | 1.7 |
| Illumina Single Cell 3’ RNA Prep T10 kit with 8 samples with 89,372 cells, 40,371 features and 513.4 MB | 0.2 | 1.8 |
Default: Illumina Spatial Transcriptomics
DRAGEN secondary analysis provides tertiary calculations used as inputs to Connected Multiomics default workflow. If recalculation is needed, additional compute is required. See [DRAGEN Secondary Analysis Compute and Storage](#dragen-secondary-analysis-compute-and-storage) for more detail about DRAGEN pipeline compute charges
| Assay | iCredits Per Sample | Total iCredits |
| ----------------------------------------------------------------------------------------------- | ------------------- | -------------- |
| Illumina spatial transcriptome technology with 1 sample that has 380k cells and approx 5B reads | 0.01 | 0.01 |
Default: Illumina Bulk Transcriptomics
Compute needs vary based on number of features and reads obtained.
| Assay | iCredits Per Sample | Total iCredits |
| ---------------------------------------------------------------------------------------- | ------------------- | -------------- |
| Illumina Stranded mRNA Prep with 61 samples that has 45,493 transcripts and 12 MB | <0.01 | 0.22 |
| Illumina Stranded Prep with 8 samples that has 42,767 transcripts and 4.32 MB | <0.01 | 0.05 |
| Illumina Stranded Total RNA Prep with 18 samples that has 39,466 transcripts and 5.41 MB | <0.01 | 0.07 |
Default: Illumina miRNA
Compute needs vary based on number of features and reads obtained.
| Assay | iCredits Per Sample | Total iCredits |
| ---------------------------------------------------------------- | ------------------- | -------------- |
| Illumina miRNA with 6 samples with 821 features and \~102M reads | <0.01 | <0.01 |
| Illumina miRNA with 96 samples with 821 features | <0.01 | <0.01 |
Default: Illumina 5-Base DNA
Varies based on sequencing depth and Germline versus Somatic differences
| Assay | iCredits Per Sample | Total iCredits |
| --------------------------------------------------------------------------- | ------------------- | -------------- |
| Methylome only (6 samples) | 0.17 | 1.03 |
| Germline 5-Base Genome
(SNV + CNV + SV) at 35-40X (23 samples)
| 0.72 | 16.53 |
| Methylome + Tumor-only Somatic VC at >100x (8 samples) | 0.44 | 3.53 |
| Targeted Somatic SNVs + Methylation (1MB panel) at > 100x (24 samples) | 0.006 | 0.15 |
### :arrow-progress: Custom Workflows
Custom: Illumina Proteomics
Based on Tutorial Study **Illumina Protein Prep (Custom)**.
| Function | iCredits Consumed | Time |
| --------------------------------- | ----------------- | ------ |
| Import | 0.08 | |
| Filtered Counts | 0 | 3 sec |
| Features in Gene Symbol List | 0 | 3 sec |
| Normalized counts | 0 | 1 sec |
| GSEA | 0 | 18 sec |
| Limma-trend | 0 | 20 sec |
| PCA | 0 | 4 sec |
| Hierarchical clustering / heatmap | 0 | 1 sec |
| Pathway enrichment | 0.02 | 1 sec |
| **Total iCredits** | 0.1 | |
Custom: Illumina Infinium Methylation
Based on Tutorial Study **Illumina Infinium Methylation (Custom)** with 60 samples of Methylation Screening Array
| Function | iCredits Consumed | Time |
| --------------------------------- | ----------------- | ------------ |
| Import | 0.07 | 23 sec |
| Generate beta value | 0 | 47 sec |
| Different methylation | 0.4 | 5 min 51 sec |
| Filter | 0 | 19 sec |
| PCA | 0 | 11 sec |
| Hierarchical clustering / heatmap | 0 | 1 sec |
| Pathway enrichment | 0 | 3 sec |
| **Total iCredits** | 0.47 | |
Custom: Illumina Single Cell Transcriptomics
Based on Tutorial Study **Illumina Single Cell 3' Prep (Default)**.
| Function | iCredits Consumed | Time |
| ---------------------- | ----------------- | ------------- |
| Import | 1.8 | 41 min 28 sec |
| Normalization | 0.6 | 24 min 24 sec |
| PCA | 5.4 | 97 min 42 sec |
| Graph-based clustering | 0.8 | 10 min 55 sec |
| Compute biomarkers | 2.9 | 68 min 23 sec |
| UMAP | 0.01 | 1 min 37 sec |
| **Total iCredits** | 9.72 | |
Custom: Illumina Spatial Transcriptomics
Based on Tutorial Study Illumina Spatial Transcriptome.
| Function | iCredits Consumed | Time |
| -------------------------------------- | ----------------- | ------------- |
| Import | 0 | 34 sec |
| Spatial report | 0 | 0 sec |
| Filter observations | 0.09 | 1 min 13 sec |
| Filter Features | 1.33 | 24 min 45 sec |
| Normalization | 0.48 | 29 min 6 sec |
| ScType cell classification | 0.17 | 1 min 14 sec |
| BANKSY - Spatial Domain Identification | 3.08 | 43 min 23 sec |
| ANOVA | 1.06 | 9 min 31 sec |
| Differential analysis filter | 0.46 | 6 min 32 sec |
| Correlation Engine pathway | 0.13 | 22 min 27 sec |
| **Total iCredits** | 6.80 | |
Custom: Illumina Bulk Transcriptomics
Based on Tutorial Study **Illumina Stranded Total RNA Prep (Custom)**.
| Function | iCredits Consumed | Time |
| ----------------------------------------- | ----------------- | ------- |
| Import | 0.05 | 20 sec |
| Annotate features | < 0.01 | 1 sec |
| Normalization | < 0.01 | 2 sec |
| PCA | < 0.01 | 2 sec |
| Differential analysis | < 0.01 | 15 sec |
| Filtering differential expression results | < 0.01 | 3 sec |
| Gene set enrichment | < 0.01 | 4 sec |
| Pathway analysis | < 0.01 | < 1 sec |
| Heatmap | 0.02 | 16 sec |
| Bubble map | < 0.01 | 12 sec |
| **Total iCredits** | 0.07 | |
Custom: Illumina miRNA
Based on Tutorial Study (6 samples, 821 features).
| Function | iCredits Consumed | Time |
| ----------------------- | ----------------- | ----- |
| Normalization | 0 | 1 sec |
| PCA | 0 | 3 sec |
| Hierarchical clustering | 0 | 2 sec |
| **Total iCredits** | <0.01 | |
Custom: Illumina 5-Base DNA (Methylome only)
6 samples, Methylome only
| Function | iCredits Consumed Per Sample | Time Per Analysis (6 samples) |
| ----------------------------------------------------- | ---------------------------- | ----------------------------- |
| Import 5-base methylation data into a custom analysis | 0.165 | 25 min 50 sec |
| 5-base methylation QC report | 0 | 0 sec |
| PCA | 0.03 | 2 min 53 sec |
| DSS | 0.47 | 49 min 26 sec |
| Filter DSS results | 0.01 | 6 sec |
| Annotate regions | 0 | 1 sec |
| Gene set enrichment | 0 | 1 sec |
| **Total iCredits** | 0.675 | |
Custom: Illumina 5-Base DNA (Germline 5-Base Genome)
Germline 5-Base Genome (SNV + CNV + SV) at 35-40X, 23 samples
| Function | iCredits Consumed Per Sample | Time Per Analysis (23 samples) |
| ----------------------------------------------------- | ---------------------------- | ------------------------------ |
| Import 5-base methylation data into a custom analysis | 0.41 | 166 min |
| 5-base methylation QC report | 0 | 0 sec |
| Filter counts | 0.0004 | 39 sec |
| PCA | 0.03 | 10 min 21 sec |
| DSS | 0.003 | 2 min 53 sec |
| Filter DSS results | 0 | 1 sec |
| Annotate regions | 0 | 2 sec |
| Filter variants | 0.01 | 2 min 56 sec |
| Summarized cohort mutations | 0.008 | 16 min 52 sec |
| Remove background mutations | 0.006 | 11 min 43 sec |
| Annotate variants | 0.017 | 70 min 23 sec |
| Combine 5-base methylation and variant data | 0.075 | 24 min 17 sec |
| **Total iCredits** | 0.556 | |
Custom: Illumina 5-Base DNA (Methylome + Tumor-only Somatic VC)
Methylome + Tumor-only Somatic VC at >100x, 8 samples
| Function | iCredits Consumed Per Sample | Time Per Analysis (8 samples) |
| ----------------------------------------------------- | ---------------------------- | ----------------------------- |
| Import 5-base methylation data into a custom analysis | 0.276 | 94 min 30 sec |
| 5-base methylation QC report | 0 | 0 sec |
| PCA | 0.023 | 2 min 59 sec |
| DSS | 0.425 | 64 min 36 sec |
| Filter DSS results | 0 | 3 sec |
| Annotate regions | 0 | 1 sec |
| Filter variants | 0 | 1 min 4 sec |
| Summarized cohort mutations | 0.005 | 4 min 21 sec |
| Remove background mutations | 0.008 | 9 min 53 sec |
| Annotate variants | 0.009 | 12 min 43 sec |
| Combine 5-base methylation and variant data | 0.584 | 65 min 48 sec |
| Gene set enrichment | 0 | 15 sec |
| **Total iCredits** | 1.33 | |
Custom: Illumina 5-Base DNA (Targeted Somatic SNVs + Methylation)
Targeted Somatic SNVs + Methylation (1MB panel) at > 100x, 24 samples
| Function | iCredits Consumed Per Sample | Time Per Analysis (24 samples) |
| ----------------------------------------------------- | ---------------------------- | ------------------------------ |
| Import 5-base methylation data into a custom analysis | 0.024 | 38 min 19 sec |
| 5-base methylation QC report | 0 | 0 sec |
| PCA | 0.017 | 6 min 4 sec |
| DSS | 0.028 | 10 min 28 sec |
| Filter DSS results | 0 | 2 sec |
| Annotate regions | 0 | 1 sec |
| Filter variants | 0 | 2 sec |
| Summarized cohort mutations | 0 | 1 sec |
| Remove background mutations | 0.001 | 6 min 27 sec |
| Annotate variants | 0 | 3 sec |
| Combine 5-base methylation and variant data | 0 | 0 sec |
| Gene set enrichment | 0 | 1 sec |
| **Total iCredits** | 0.07 | |
### 
DRAGEN Secondary Analysis Compute and Storage
DRAGEN Protein Quantification
DRAGEN Protein Quantification is no charge for compute as these charges are included in the assay kit purchase.
| Assay | Compute in Credits Per Sample | Storage per month in iCredits |
| -------------------------- | ----------------------------- | ----------------------------- |
| Illumina Protein Prep 9.5K | 0 | <0.01 |
DRAGEN Single Cell RNA
DRAGEN Single Cell RNA is no charge for compute as these charges are included in the assay kit purchase. Estimated storage costs below include outputs from a DRAGEN Single Cell RNA analysis with the default options (no BAM output is generated by default).
| Assay | Compute in Credits Per Sample | Storage per month in iCredits |
| -------------------------------------------------------------------------------------------------------------- | ----------------------------- | ----------------------------- |
| Illumina Single Cell 3’ RNA Prep T100 kit with 2 sample that has 318,910 cells and 40,371 features and 2.19 GB | 0 | 0.16 |
| Illumina Single Cell 3’ RNA Prep T20 kit with 4 samples with 99,570 cells, 40,563 features, and 587.7 MB | 0 | 0.08 |
| Illumina Single Cell 3’ RNA Prep T10 kit with 8 samples with 89,372 cells, 40,371 features and 513.4 MB | 0 | .04 |
DRAGEN Spatial Transcriptome
Available to early access customers only.
| Assay | Compute in Credits for Total Samples | Compute in Credits Per Sample | Storage per month in iCredits |
| ---------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------ | ----------------------------- | ----------------------------- |
| Illumina Spatial Transcriptome slide with 4 mouse kidney samples (cell counts: 322k, 287k, 313k, and 277k), sequenced with one 25B | 80 | 20 | 6.1 |
| Illumina Spatial Transcriptome slide with 4 human breast samples (cell counts: 389k, 351k, 717k and 718k), sequenced with one 25B | 146 | 37 | 7.2 |
DRAGEN RNA
Varies based on input, sequencing depth and functionality run.
| Assay | Compute in Credits for Total Samples | Compute in Credits Per Sample | Storage per month in iCredits |
| ------------------------------------------------------------------------------------ | ------------------------------------ | ----------------------------- | ----------------------------- |
| NovaSeq X (10B): Illumina Stranded Total RNA with 18 samples (File size: 141.00 GB) | 33.7 | 1.9 | 3.2 |
| NovaSeq X (1.5B): Illumina Stranded mRNA prep with 61 samples (File size: 184.63 GB) | 45.0 | 0.7 | 4.2 |
DRAGEN miRNA
DRAGEN miRNA is no charge for compute as these charges are included in the assay kit purchase.
| Assay | Compute in Credits Per Sample | Storage per month in iCredits |
| ---------------------------------------------------------------------- | ----------------------------- | ----------------------------- |
| Illumina miRNA with 96 samples with 821 features (File size: 18.47 GB) | 0 | 0.4 |
| Illumina miRNA with 48 samples with 821 features (File size: 9.24 GB) | 0 | 0.2 |
DRAGEN 5-Base DNA Prep and 5-Base DNA Prep with Enrichment
Varies based on sequencing depth and functionality run.
| Assay | Compute in Credits Per Sample | Storage per month in iCredits |
| -------------------------------------------------------------- | ----------------------------- | ----------------------------- |
| Germline 5-Base Genome
(SNV + CNV + SV) at 35-40X
| 5 | 2.5 |
| Methylome + Tumor-only Somatic VC at >100x | 12 | 5 |
| Targeted Somatic SNVs + Methylation (1MB panel) at > 100x | < 1 | 1 |