FindingNemo

Compilation of R functions to produce ultra-long sequencing metrics and graphs from ONT platforms, but can be used for any nanopore sequencing output (including ligation based).
After copying/downloading into a folder, run source(functionName) to read and execute the function.
Required arguments can be called by args(functionName) command.
Annotations of the arguments are given inside every function file, below are some examples.

compileOccupancy

Calculate relative occupancies of the three types of available pores (i.e. adapter, pore, and strand)

compileOccupancy(dutyTimeFile = "path/to/duty_time_file/or/pore_activity_file", # different chemistry version calls the file differently
                 workDir = "path/to/working/directory", # better to use the location of the sequencing output folder
                 saveFile = "test_occupancy",
                 startPoint = 11, stopPoint = NULL, runStatus = "run01")

Output test_occupancy.csv file is saved in workDir.

lengthHistogram

Create a histogram of read length distribution and N50

lengthHistogram(seqSummary = "path/to/sequencing_summary_file",
                workDir = "path/to/working/directory", # better to use the location of the sequencing output folder
                runID = "run01", endTime = 60, yInt = 10, breaksStart = 2, breaksVal = 1)

Output run01_timed_histogram.png is saved in the same folder with the sequencing_summary_file.txt.

metricsTable

Calculate sequencing metrics, including normalised yield (i.e. yield per pore over a period of data collection time)

metricsTable(seqSummary = "path/to/sequencing_summary_file",
             workDir = "path/to/working/directory", # better to use the location of the sequencing output folder
             runStatus = "run01", stopPoint = 1440,
             saveDir = "path/to/output/directory",
             saveFile = "test_metrics")

Output test_metrics.csv is saved in saveDir.

yieldStack

Create a stackplot of yield based on read length categories

yieldStack(seqSummary = "path/to/sequencing_summary_file",
           workDir = "path/to/working/directory", # better to use the location of the sequencing output folder
           runID = "run01", platform = "P24", endTime = 120, ystack = 5)

Output run01_timed_stackplot.png is saved in the same folder with the sequencing_summary_file.txt.

Function compileOccupancy and metricsTable can each compile an output table consisting of multiple run data. Just change the argument parameters.