Question about sequencing type

[sounkou-bioinfo]

Hi all,

Thank you for this great tool andcopen sourcing it.
This is more of the question than an issue. I wanted to know if the method can be applied to short target capture reads (like exome sequencing) andcis it restricted to illumina sequencers in this context ? Is there a recommended aligner (e.g BWA vs Dragmap Os etc) and reads preprocessing options ?

Thank you in advance
Best

[FengheLi]

Hi,

For SRS(short-read sequencing) dataset, the input should be 100~250bp paired-end (PE) sequencing data; but for non-WGS (Whole Genome Sequencing) types of data, we have not yet conducted comprehensive testing.
We have tested our method on datasets from BGI (T7), Illumina, and PacBio (HiFi).
For short-read sequencing data, the BWA-MEM is recommended for sequence alignment. Once the FASTQ files are aligned using BWA (with default parameters) and subsequently sorted to form BAM or CRAM files, they are ready for SV detection.

[sounkou-bioinfo]

Thank you for this response @FengheLi !