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|`-tl/--target_lines`| desired file length for split fastq files (must be multiple of 4, default: 500000) |
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|`-pcr/--pcr_read_threshold`| ratio above which majority of PCR reads must be in order for a UMI to be called definitively (default: 0.5) |
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|`-z/--skip_shuf`| if set to 1, skip the random shuffling of fastq files step, useful if needing to re-run just the IronThrone and UMI collapsing components of the pipeline (default: 0)|
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|`-x/--ski_iron_throne`| if set to 1, skip the IronThrone step of the pipeline, useful if run in combination with `skip_shuf` to only run the UMI collapsing component of the pipeline (default: 0) |
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|`-x/--skip_iron_throne`| if set to 1, skip the IronThrone step of the pipeline, useful if run in combination with `skip_shuf` to only run the UMI collapsing component of the pipeline (default: 0) |
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|`-ld/--levenshtein_distance`| Allowed Levenshtein distance between UMIs determined to be similar enough for collapsing (default: 0.1) |
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