BulkSeq Studio 0.13.0

BulkSeq Studio 0.13.0

Added

• rRNA filtering with SortMeRNA. The "rRNA filtering" workflow option is now implemented (it was previously a checkbox that did nothing). When enabled, trimmed reads are filtered against the SortMeRNA rRNA database before alignment, on all three aligner routes (STAR, HISAT2, Salmon): the reference is downloaded and indexed once per project, then each sample is filtered in its own working directory and the non-rRNA reads feed the aligner. The per-sample SortMeRNA log (rRNA %) is added to the MultiQC report, and sortmerna is now part of the core environment. A custom reference can be set via sortmerna.database (a local FASTA, a FASTA URL, or a database tarball URL); the default is smr_v4.3_default_db.

Fixed

• Rule guards added in 0.12.2 could abort their own rules. The command -v … || { … } guards in make_transcriptome, salmon_index, and hisat2_index used unescaped braces, which Snakemake parses as format fields, raising a NameError and stopping the Salmon and HISAT2 routes even when the tool was present. The braces are now escaped, so those routes run. (The STAR route was never affected.)

Upgrading

The rRNA option needs sortmerna, now in the core environment: open Check Environment → Install / repair core environment (on Linux, update from workflow/envs/bulkseq_core.yaml). Enabling rRNA filtering downloads a ~150 MB reference and builds a multi-GB index once per project.

Downloads

Windows:

• BulkSeqStudio-Setup-0.13.0.exe — installer
• BulkSeqStudio-Portable-0.13.0.zip — unzip and run BulkSeqStudio.exe, no install

Linux (x86-64, glibc 2.39+):

• BulkSeqStudio-0.13.0-x86_64.AppImage — mark executable and run
• BulkSeqStudio-linux-0.13.0.tar.gz — extract and run BulkSeqStudio