Software Compatibility and Parameter Selection

[huayaozhang123]

Hello, our research sample is Vibrio cholerae. We obtained chromosome-level complete genome data by correcting third-generation ONT sequencing data using Illumina sequencing data. We would like to inquire whether this software is suitable for our data. If it is suitable, how should the parameters be adjusted for optimal results?

Thanks！

[Meltpinkg]

Hello, @huayaozhang123

cuteSV is suitable for the chromosome-level complete genome data. In this condition, we recommend to use the diploid-assembly-based SV detection in cuteSV. More details can refer to here.
The major steps contain adding haplotype-unique tags for reads from different haplotypes (details in Step 4). And when running cuteSV, we recommend to apply the parameter -s 1 --genotype --report_readid -p -1 -mi 500 -md 500 --max_cluster_bias_INS 1000 --diff_ratio_merging_INS 0.9 --max_cluster_bias_DEL 1000 --diff_ratio_merging_DEL 0.5.
If there is anything that I can help, please feel free to reach out.

Best,
Shuqi