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YEAT: Your Everyday Assembly Tool
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Hybrid #68

Closed danejo3 closed 3 months ago

danejo3 commented 5 months ago

The purpose of this PR is to introduce "hybrid" assembly to YEAT's workflow. To run hybrid mode, first, give a sample two types of reads: 1) pair-end, and 2) any kind of long read. Second, set an assembly's mode to "hybrid".

For 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"
            ]
        }
    },
    "assemblies": {
        "unicycler-hybrid": {
            "algorithm": "unicycler",
            "extra_args": "",
            "samples": [
                "Shigella_sonnei_53G"
            ],
            "mode": "hybrid"
        }
    }
}

Below is a diagram of YEAT's output dir. In green are the final files created by YEAT. (Note: the .done file in the Bandage directory will exist if Bandage is on the user's computer.)

image