search

stat-lab / EvalSVcallers

Evaluate the performances (precision and recall) of structural variation (SV) callers
32 stars 13 forks source link

Suggestion/Request: add more other SV caller using long reads #1

Closed tjiangHIT closed 4 years ago

tjiangHIT commented 5 years ago

Congratulations to you for paper publishing and thanks for your great work! You evaluate plenty of tools and give a lot of helpful viewpoints for choosing SV callers. However, in your benchmarks, only 3 approaches (sniffles, pbsv and pbhoney) are used for evaluation. I think a comparison analysis with more other existing tools using long reads will be helpful (e.g. SVIM, a newer caller for SV detection; rMETL, a non-reference MEI detector.). In a sense, it is difficult to search SV callers based on 3rd generation sequencing compared with NGS.

Hope your reply! Tao

stat-lab commented 5 years ago

Dear Tao,

Thank you for your comment. New SV callers will be developed and new versions of existing tools will be updated after our paper has been published. We will make an effort to continue updating our evaluation results, integrating results of new SV callers, and to present them at this site.

2019/06/04 15:42、JiangTao notifications@github.comのメール:

Congratulations to you for paper publishing and thanks for your great work! You evaluate plenty of tools and give a lot of helpful viewpoints for choosing SV callers. However, in your benchmarks, only 3 approaches (sniffles, pbsv and pbhoney) are used for evaluation. I think a comparison analysis with more other existing tools using long reads will be helpful (e.g. SVIM https://github.com/eldariont/svim, a newer caller for SV detection; rMETL https://github.com/tjiangHIT/rMETL, a non-reference MEI detector.). In a sense, it is difficult to search SV callers based on 3rd generation sequencing compared with NGS.

Hope your reply! Tao

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/stat-lab/EvalSVcallers/issues/1?email_source=notifications&email_token=ADIBV3DU372Z5BDMQIWVGKTPYYFFXA5CNFSM4HSZHWKKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4GXOI6RA, or mute the thread https://github.com/notifications/unsubscribe-auth/ADIBV3GOUTQID5M2UWJ3U53PYYFFXANCNFSM4HSZHWKA.

tjiangHIT commented 5 years ago

Hi @stat-lab , Thanks for your prompt response! It is a valuable work for promoting developing SV callers with higher sensitivity and accuracy. Looking forward to your update.

Cheers! Tao

Tintest commented 5 years ago

Hello,

I approve @tjiangHIT's request to add more long reads SV caller. If you could add SVIM , npInv and NanoSv in your tool list it would be great !

Regards.