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:
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 type:
- Output type:
The default input parameter for FastQ data is
--fastq. You can change
--fastq parameter default pattern (
to input file names (e.g.:
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.
reports/coverage: CSV table with estimated sequencing coverage for each sample.