Hybrid assembly

Currently, the only algorithm in YEAT that supports hybrid assembly is Unicycler. To enable this mode, make the following changes to the configuration file:

1. Add two types of reads to the sample:
   • Paired-end reads
   • Any type of long read
2. Set the Unicycler assembly "mode" to "hybrid".

Example

{
    "samples": {
        "Shigella_sonnei_53G": {
            "paired": [
                ["yeat/tests/data/short_reads_1.fastq.gz", "yeat/tests/data/short_reads_2.fastq.gz"]
            ],
            "pacbio-corr": [
                "yeat/tests/data/long_reads_high_depth.fastq.gz"
            ],
            "downsample": 0,
            "genome_size": 0,
            "coverage_depth": 150
        }
    },
    "assemblies": {
        "unicycler-hybrid": {
            "algorithm": "unicycler",
            "extra_args": "",
            "samples": [
                "Shigella_sonnei_53G"
            ],
            "mode": "hybrid"
        }
    }
}