v2.1.3

New in SpeciesPrimer v2.1.3

• use NCBI datasets to download genomes (assembly db End-of-Life by NCBI)
• EOL of SpeciesPrimer GUI. Please use the command line. (see Command line options)

SpeciesPrimer v2.2-beta.5

New in SpeciesPrimer v2.2-beta.5

• Updated dependencies
• Docker runs as user (not root)
  New in SpeciesPrimer v2.2
• Automatic download of genome assemblies from genbank
• New filter options for specificity BLAST step
  • Nucleotide identity
  • E-value
• New functions (experimental)
  • StrainPrimer: strain specific primer design
  • Primer design for viruses (no input QC!)
• Removed blastdbv5 option
  • v5 BLAST DB is the new standard
  • Taxid filtering is not supported anymore (use customdb instead)
• Bugfixes

SpeciesPrimer v2.2-beta.4

• Include pathovar keyword
• Use in format Genus_species_pv_identifier
  Example:

speciesprimer.py -t Pseudomonas_syringae_pv_syringae

v2.2-beta.3

Bugfix

SpeciesPrimer v2.2-beta.2

New in SpeciesPrimer v2.2

• Automatic download of genome assemblies from genbank
• New filter options for specificity BLAST step
  • Nucleotide identity
  • E-value
• New functions (Beta)
  • Strainprimer: strain specific primer design
  • Primer design for viruses
• Removed blastdbv5 option
  • v5 BLAST DB is the new standard
  • Taxid filtering is not supported anymore (use customdb instead)
• Bugfixes

SpeciesPrimer v2.2-beta.1

New in SpeciesPrimer v2.2

• Automatic download of genome assemblies from genbank
• New filter options for specificity BLAST step
  • Nucleotide identity
  • E-value
• New functions (Beta)
  • Strainprimer: strain specific primer design
  • Primer design for viruses
• Removed blastdbv5 option
  • v5 BLAST DB is the new standard
  • Taxid filtering is not supported anymore (use customdb instead)
• Bugfixes

SpeciesPrimer v2.1.2

• Update scripts for new BLAST database names and arrangement on the NCBI FTP site
• The standard BLAST database version is now 5!
• for more information see https://ncbiinsights.ncbi.nlm.nih.gov/2020/01/28/blast-db-ftp/

SpeciesPrimer v2.1.1

• Configfile option for pipeline setu
• Custom Blast DB support
• Email option for command line
• Increased speed
• Species synonyms are added to exceptions
• Bugfixes and KeyboardInterrupt rollback
• Simpler directory structure

SpeciesPrimer v2.1

SpeciesPrimer v2.1

• Custom Blast DB support
• Email option for command line
• Increased speed
• Species synonyms are added to exceptions
• Bugfixes and KeyboardInterrupt rollback
• Simpler directory structure

SpeciesPrimer v2.01

Bugfixes

• fixed exception species handling during QC