General information and Q&A
How are SVs detected?
SVs are detected by identifying pattern differences between the query and the reference, usually based on pair-wise alignment.
Should I use optical maps or optical mapping assemblies as query?
You can use either or both. Here are some pros and cons of the query choice.
Table 1. Pros and cons of query choice on SV detection.
| Query choice | Optical maps (Molecules) | Optical mapping assemblies |
|---|---|---|
| Haplotype detection | Yes | Yes, only if the assembly process is haplotype-sensitive |
| Potential source of bias | Inaccurate alignment | Inaccurate assembly Inaccurate alignment |
| Detection of very large SVs* | No | Yes |
*Here, very large SVs refer to those SVs larger than the optical maps, making it impossible for optical maps to flank across them.
Can I use SV detection to detect sequence mis-assembly?
Yes, SV detection can be applied on identifying sequence mis-assembly. You need to set the alignment reference to in-silico digested sequence scaffolds, and alignment query to optical maps or optical mapping assemblies from the same sample.
What types of SVs can I detect?
You can detect insertions, deletions, inversions, copy number variations and translocations.
Can I use optical mapping to detect SNPs?
No. SNPs are too small to affect the optical mapping patterns. Only in rare occasion, SNPs that disrupt an existing nicking enzyme site or create a new nicking enzyme site lead to change in pattern.
Can I detect SVs across species?
It depends on how different the genome structures are between two species. In most cases, genome structures from two species are too dissimilar for comparison.
Can I obtain the sequence of the SVs from detection results based on optical mapping?
No, you cannot get the sequence information just based on optical mapping. Additional data such as sequencing results or reference sequences is usually needed to deduce the sequence of detected SVs.
How can I deduce the sequence of a detected SV?
You could use long-range PCR (Polymerase chain reaction) to amplify the region that contains the target SV, followed by sequencing of the products. Alternatively, if you have high-throughput sequencing data of the same sample, you could determine the corresponding sequence based on the alignment of optical mapping assemblies and sequence assemblies.
Detailed commands
Please refer to the OMSV website for detailed commands.