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README.md

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`CycSim` takes a genome assembly file and a trained model file as input to generate simulated reads in BAM format.
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```sh
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../target/release/cycsim sim -t 60 -d 30 model.cy ref.fa -o sim.bam
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./target/release/cycsim sim -t 60 -d 30 model.cy ref.fa -o sim.bam
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```
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***Note:*** If you need to simulate more than 50× coverage (i.e., more than the depth used for training), it is recommended to add the `-n` option. This will introduce additional random errors and help avoid oversampling artifacts.
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`CycSim` can be trained to build an error model from real sequencing data. It takes a genome assembly file and a read mapping file in BAM format as input (sorting is not required) and produces a trained model file.
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```sh
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../target/release/cycsim train -t 60 -r nanopore read.bam ref.fa -o model.cy
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./target/release/cycsim train -t 60 -r nanopore read.bam ref.fa -o model.cy
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```
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Use `./target/release/cycsim -h` to see options.

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