BIONUMERICS version 8.1.1

Version 8.1.1 of BIONUMERICS (detailed version 8.1.1 build 32234.42204) is now available for download. You can request a price quote to upgrade your current version 7.6 to 8.1.1.

Instructions for installation

Important: Before proceeding with the installation, please make sure to obtain a license string for version 8.1.

  1. Click on the link above to download the update.
  2. Close BIONUMERICS.
  3. Double-click on the executable to run the setup. Please note that this action will require administrator privileges.

List of improvements

REMINDER: The BIONUMERICS software is phasing out and version 8.1.1 is the final BIONUMERICS release, which will be supported until the end of 2024.

Improvements in version 8.1.1 build 8.1.1.32234.42204:

The only change in this build compared to the previous version is a fix for the “None of the accession codes could not be found on NCBI (SRA)” error that occurred during import of sequence read sets from SRA and submission of jobs with SRA data. Installing this build makes it unnecessary to apply the hotfix for importing sequence read sets from NCBI in each individual BIONUMERICS database.

Improvements in version 8.1.1 build 8.1.1.31729.42196:

  • Fix for local calculation engine jobs receiving the status “Dead” on systems with a French Windows version installed.
  • Local calculation engine jobs run without errors again on fastq.gz files with spaces in the file path.
  • MS Excel files containing non-ASCII characters in the file name can be imported again.
  • Additional input validation in the Custom genotyping plugin to ensure that model or feature names do not contain spaces.
  • The import of gel images can be initiated again via the “plus” icon in Fingerprint files panel.
  • Additional requirement for the Microsoft Visual C++ Redistributable package (x64) in the BIONUMERICS installer to ensure all dependencies for the SNAP open source sequence aligner are met.

New functionality in version 8.1.1 build 8.1.1.31463.42184:

New MLST for WGS plugin

As the name suggests, the new MLST for WGS plugin is specifically designed for performing MLST analysis with whole genome sequences as input. Based on the genotyping framework, it performs a fast, accurate and complete allele calling and allows running multiple MLST schemes in a single database.

Similar as for the MLST for Sanger sequencing plugin (formerly known as the “MLST online plugin”), the MLST for WGS plugin allows you to select MLST schemes from an online list and to create and maintain custom MLST schemes.

File first approach for import

The import wizard now includes an additional dialog that allows you to browse for your data files and suggests suitable import routines, based on file type and content. This new feature greatly facilitates the import process and makes it more intuitive by eliminating the need to select the required import routine in the tree overview with all possible imports.

Long read only de novo assembly

In addition to hybrid assembly (i.e., combining short and long reads in a single assembly) that was introduced earlier, it is now possible to perform long read only assemblies on e.g. PacBio and NanoPore sequence reads. This feature is implemented on the Calculation Engine via the open source Unicycler de novo assembler.

Other new features:

  • The E. coli, Listeria, Salmonella and Staphylococcus aureus genotyping plugins were extended with a species confirmation feature using minhashing, which checks if an isolate is indeed a target organism for the plugin.
  • To extend the serviceable life of this final BIONUMERICS version, the concept of online plugins is reintroduced and plugins stored in the database take precedence over plugins in the installation directory.
  • The download of sequence read data from NCBI SRA is improved and made faster.
  • SQLite databases can be compacted without the need for third-party software.
  • Calculation Engine job logs can be removed in bulk to reduce database sizes.
  • The open source tool fastp is now used for trimming sequence read sets on the Calculation Engine and local Calculation Engine.
  • Sequences can be imported from zipped files, such as TAR archives downloaded from NCBI Assemblies.
  • An additional filter is made available in the Comparison window to filter characters based on their value.
  • The Custom genotyping plugin is extended with mutational resistance and species confirmation features.
  • In the Fast matching window, a command is added to select all matches with the screened entries for further analysis in the Comparison window.
  • The used character set can again be specified in the Preferences window. This is mainly important for Chinese and Japanese language users.
  • In the Contigs panel of the Sequence viewer, contigs can be sorted according to size.

For an overview of all new features in the latest version, see following release notes: