downsample_fastq¶
Purpose¶
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/Output type¶
- Input type:
fastq
- Output type:
fastq
Parameters¶
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.
Published results¶
results/sample_fastq
: Stores the subsampled FastQ files
Published reports¶
None.
Default directives¶
cpus
: 1memory
: 4GBcontainer
: flowcraft/seqtkversion
: 1.3.0-3