Statistics¶
Usage¶
At any time a user with the staff permission and higher can access the interactive statistics to monitor usage of laboratory and workflows for a chosen period of time. Choose “Usage” in the navigation panel on the left side and set a date range. Pie charts illustrate proportions of submitted samples and libraries, organizations, principal investigators and library types. Bar charts represent the number of submitted samples or libraries per principle investigator or library type. Any chart can be downloaded as png file.
Runs and Sequences¶
To evaluate the success of a given sequencing run specifications are imported into Parkour LIMS and shown in the tabs runs and sequences. Note that Parkour mainly imports and displays the listed parameters. Calculations are done using non-Parkour software and scripts.
Runs¶
To view run specifications, navigate to the “Runs” tab and select a time range.
| Parameter | Explanation |
|---|---|
| Lane | The lane number on the flowcell. Lane number will depend on the sequencing instrument in use. MiSeq: 1 lane, HiSeq2500 Rapid: 2 lanes, NextSeq: 4 lanes, HiSeq3000: 8 lanes. |
| Pool | Information on pool loaded on a given lane. Per lane only one pool can be loaded. |
| Request | Information on request(s) loaded on a given lane |
| Preparation Method | Information on library preparation method |
| Library Type | Information on library type |
| Loading Concentration | DNA loading concentration per lane |
| Cluster Pass Filter (PF) %* | Percentage of clusters passing Illumina’s quality filter |
| Reads PF (%)* | Percentage of reads (read-pairs for paired-end datasets) passing quality filter |
| Undetermined Indeces (%)* | Percentage of undetermined indeces after demultiplexing |
| Spike-In (%)* | Percentage of Spike-In used to accomplish nucleotide diversity (typically PhiX library, Illumina) |
| Read 1 % bases >= Q30* | Quality measure for read 1, percentage of bases in read 1 having a Phred-scaled score of at least 30 |
| Read 2 % bases >= Q30* | Quality measure for read 2, Êpercentage of bases in read 2 having a Phred-scaled score of at least 30 |
Sequences¶
To assess quality of each sequenced sample, navigate to “Sequences” tab. To download parameters into a spreadsheet, check samples and click “Download Report”.
| Parameter | Explanation |
|---|---|
| Request | Running number and information on user and principal investigator |
| Barcode | Sample barcode, running number automatically generated from Parkour upon request generation |
| Name | Sample name given by user |
| Lane | Lane number sample was sequenced on |
| Pool | Group of samples the sequenced sample was part of |
| Library Protocol | Information on library preparation method |
| Library Type | Information on library type |
| Reads (M) (requested) | Number of read (read-pairs for paired end sequencing) requested by user |
| Reads (M) sequenced* | Number of reads (read-pairs for paired end sequencing) generated by sequencer |
| Confident off-species reads* | Percentage of reads uniquely aligned to another, but the target organism |
| % optical duplictes* | Percentage of duplicates in nearby wells on patterned flowcells. Reason: During cluster generation a library can occupy two adjacent wells |
| % dupped reads* | Percentage of duplicated reads |