Can LexicMap being used for reads mapping to caculate genome or gene abundance？

[Caiyulu-818]

Hello,

Thank you for developing LexicMap, it looks like a very promising tool for large-scale sequence search. I would like to ask whether LexicMap can also be applied to short read mapping tasks, for example, mapping metagenomic reads to a reference database in order to estimate genome or gene abundance.
• Is LexicMap designed to support this type of application (read-to-reference alignment/quantification)?
• If not directly, do you have any recommendations on how LexicMap could be integrated into such workflows?
• Are there plans to extend LexicMap towards quantitative applications (e.g., abundance estimation)?

Thanks a lot for your time and for sharing this tool with the community!

Best regards
Caiyu

[shenwei356]

Thanks for your attention.

whether LexicMap can also be applied to short read mapping tasks

Does LexicMap support short reads?
LexicMap is mainly designed for sequence alignment with a small number of queries (gene/plasmid/virus/phage sequences) longer than 150 bp by default.

Is LexicMap designed to support this type of application (read-to-reference alignment/quantification)?

No. Users need to perform quantification themselves.

If not directly, do you have any recommendations on how LexicMap could be integrated into such workflows?

No. Other tools might help.

Are there plans to extend LexicMap towards quantitative applications (e.g., abundance estimation)?

No.