SNPEff database athaliana130

Question

[mlogotheti]

Hello to everyone,

I would like to ask the following question: I can only identify the snpEff_v4_3_athaliana130.zip database (unfortunately not TAR10 snpEff database) in the 4.3 version of snpEff, but I can not figure out the corresponding arabidopsis thaliana assembly. Does anyone have a link for information about this specific genome version?

Best regards, Mar

Answer 1

[h.mon]

According to the DBHi-BiC/snpEff repository (an indirect source and not the official snpEff repository), it is an old Phytozome version:

# Arabidopsis Thaliana
athaliana130.genome : Arabidopsis_Thaliana
    athaliana130.reference : http://www.phytozome.net/dataUsagePolicy.php?org=Org_Athaliana
athaliana130.M.codonTable : Standard

However, using snpEff 4.3t, apparently there is a newer A. thaliana database version:

java -jar snpEff.jar databases | grep "Arabidopsis"

Arabidopsis_lyrata    Arabidopsis_lyrata    ENSEMBL_BFMPP_32_24    http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_ENSEMBL_BFMPP_32_24.zip
Arabidopsis_thaliana    Arabidopsis_thaliana    ENSEMBL_BFMPP_32_24    http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_ENSEMBL_BFMPP_32_24.zip
  

[mlogotheti]

Τhank you very much for you answer! I will have to find also the corresponding genome assembly.