# 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.

None.

## Published reports¶

• reports/coverage: CSV table with estimated sequencing coverage for each sample.

## Default directives¶

None.

flowcraft.templates.integrity_coverage
tableRow:
• Coverage: Estimated coverage.
fail: