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:
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}.*"
).
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.
None.
reports/coverage
: CSV table with estimated sequencing coverage for each sample.
None.
flowcraft.templates.integrity_coverage
tableRow
:Coverage
: Estimated coverage.
fail
:- When estimated coverage is below the provided threshold.