check_coverage¶
Purpose¶
This components estimates the coverage of a given sample based on the number of base pairs in the FastQ files of a sample and on the expected genome size:
\[\frac{\text{number of base pairs}}{(\text{genome size} \times 1e^{6})}\]
If the estimated coverage of a given sample falls bellow the provided minimum coverage threshold, the sample is filtered and does not proceed in the pipeline.
Input/Output type¶
- Input type:
FastQ - Output type:
FastQ
Note
The default input parameter for FastQ data is --fastq. You can change
the --fastq parameter default pattern (fastq/*_{1,2}.*) according
to input file names (e.g.: --fastq "path/to/fastq/*R{1,2}.*").
Parameters¶
genomeSize: Genome size estimate for the samples. It is used to estimate the coverage and other assembly parameters and checks.minCoverage: Minimum coverage for a sample to proceed. Can be set to 0 to allow any coverage.
Published results¶
None.
Published reports¶
reports/coverage: CSV table with estimated sequencing coverage for each sample.
Default directives¶
None.