downsample_fastq uses seqtk to subsample fastq read data to a target coverage depth if the estimated coverage is higher than the provided target depth. When no subsample is required, it outputs the original FastQ files.
Note
Software page: https://github.com/lh3/seqtk
- Input type:
fastq
- Output type:
fastq
genomeSize
: Genome size estimate for the samples. It is used to estimate the coverage.depth
: The target depth to which the reads should be subsampled.seed
: The seed number for seqtk. By default it is 100.
results/sample_fastq
: Stores the subsampled FastQ files
None.
cpus
: 1memory
: 4GBcontainer
: flowcraft/seqtkversion
: 1.3.0-3
tableRow
:Coverage
: Estimated coverage.