diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.2.0-2023a.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.2.0-2023a.yml
index a20e25a452..e7841fc573 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.2.0-2023a.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.2.0-2023a.yml
@@ -41,3 +41,10 @@ easyconfigs:
         include-easyblocks-from-commit: 0f75bae68e0323d7053e0e2dddb03e6422e666e2
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/25220
         from-commit: fc6e46c10d6c5d92ea2ab403bfcde364828fa693
+  - ABySS-2.3.7-foss-2023a.eb
+  - BUSCO-5.8.2-foss-2023a.eb
+  - cooltools-0.7.1-foss-2023a.eb
+  - Trim_Galore-0.6.10-GCCcore-12.3.0.eb
+  - Kalign-3.4.0-GCCcore-12.3.0.eb
+  - PyBioLib-1.2.205-GCCcore-12.3.0.eb
+  - CDBtools-0.99-GCC-12.3.0.eb
diff --git a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.2.0-2023b.yml b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.2.0-2023b.yml
index 90277f39e8..533b0b38f7 100644
--- a/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.2.0-2023b.yml
+++ b/easystacks/software.eessi.io/2023.06/eessi-2023.06-eb-5.2.0-2023b.yml
@@ -3,4 +3,10 @@ easyconfigs:
   - FEniCS-DOLFINx-Python-0.9.0-foss-2023b.eb:
       options:
         # see https://github.com/easybuilders/easybuild-easyconfigs/pull/25004
-        from-commit: 2ef62609e3e40785dfb28bcb91db143cee5924a5
\ No newline at end of file
+        from-commit: 2ef62609e3e40785dfb28bcb91db143cee5924a5
+  - DIAMOND-2.1.9-GCC-13.2.0.eb
+  - VSEARCH-2.30.0-GCC-13.2.0.eb
+  - HH-suite-3.3.0-gompi-2023b.eb
+  - tabix-0.2.6-GCCcore-13.2.0.eb
+  - MACS2-2.2.9.1-foss-2023b.eb
+  - cwltool-3.1.20250110105449-foss-2023b.eb
diff --git a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.2.0-2024a.yml b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.2.0-2024a.yml
index 97918e347b..d158253581 100644
--- a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.2.0-2024a.yml
+++ b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.2.0-2024a.yml
@@ -18,3 +18,27 @@ easyconfigs:
   # - framework PR for fix: https://github.com/easybuilders/easybuild-framework/pull/5142
   # - triggered by https://github.com/easybuilders/easybuild-easyblocks/pull/3993
   - jupyterlmod-5.2.2-GCCcore-13.3.0.eb
+  - cutadapt-5.1-GCCcore-13.3.0.eb
+  - deepTools-3.5.5-gfbf-2024a.eb
+  - SEPP-4.5.5-foss-2024a.eb
+  - IQ-TREE-3.0.1-gompi-2024a.eb
+  - k8-1.2-GCCcore-13.3.0.eb
+  - HTSeq-2.0.9-foss-2024a.eb
+  - MultiQC-1.28-gfbf-2024a.eb
+  - freebayes-1.3.7-gfbf-2024a-R-4.4.2.eb
+  - SearchGUI-4.3.9-GCCcore-13.3.0-Java-11.eb
+  - StringTie-3.0.0-GCC-13.3.0.eb
+  - Unicycler-0.5.1-gompi-2024a.eb
+  - snpEff-5.4c-GCCcore-13.3.0-Java-21.eb
+  - MUSCLE-5.1.0-GCCcore-13.3.0.eb
+  - GenomeTools-1.6.5-GCC-13.3.0.eb
+  - QUAST-5.3.0-gfbf-2024a.eb
+  - Trinity-2.15.2-foss-2024a-Java-17.eb
+  - PyHMMER-0.12.0-gompi-2024a.eb
+  - vcflib-1.0.9-gfbf-2024a-R-4.4.2.eb
+  - mlst-2.32.2-foss-2024a.eb
+  - GlimmerHMM-3.0.4c-GCC-13.3.0.eb
+  - RGI-6.0.6-gfbf-2024a.eb
+  - MACS3-3.0.3-gfbf-2024a.eb
+  - MetaPhlAn-4.1.1-foss-2024a.eb
+  - Kraken2-2.1.6-gompi-2024a.eb
diff --git a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-001-system.yml b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-001-system.yml
index 446ebf605a..aed582a519 100644
--- a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-001-system.yml
+++ b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-001-system.yml
@@ -1,2 +1,6 @@
 easyconfigs:
   - Julia-1.12.2.eb
+  - picard-3.4.0-Java-21.eb
+  - FastQC-0.12.1-Java-11.eb
+  - Trimmomatic-0.40-Java-17.eb
+  - Nextflow-25.10.2.eb
diff --git a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025a.yml b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025a.yml
index e6714f35a0..a44b041383 100644
--- a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025a.yml
+++ b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025a.yml
@@ -2,3 +2,19 @@ easyconfigs:
   - imageio-2.37.0-gfbf-2025a.eb
   - scikit-image-0.25.0-foss-2025a.eb
   - elfutils-0.193-GCCcore-14.2.0.eb
+  - MEME-5.5.9-gompi-2025a.eb
+  - BBMap-39.19-GCC-14.2.0.eb
+  - snakemake-9.14.0-foss-2025a.eb
+  - FastTree-2.2-GCCcore-14.2.0.eb
+  - RAxML-8.2.13-gompi-2025a.eb
+  - pybedtools-0.12.0-foss-2025a.eb
+  - cyvcf2-0.32.1-gfbf-2025a.eb
+  - DendroPy-5.0.8-GCCcore-14.2.0.eb
+  - seqtk-1.5-GCC-14.2.0.eb
+  - VCFtools-0.1.17-GCC-14.2.0.eb
+  - GMAP-GSNAP-2025-07-31-GCC-14.2.0.eb
+  - prodigal-2.6.3-GCCcore-14.2.0.eb
+  - Infernal-1.1.5-gompi-2025a.eb
+  - kallisto-0.51.1-gompi-2025a.eb
+  - prokka-1.15.6-gompi-2025a.eb
+  - snakemake-9.14.0-foss-2025a.eb
diff --git a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml
index 03898164f3..9b439380c6 100644
--- a/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml
+++ b/easystacks/software.eessi.io/2025.06/eessi-2025.06-eb-5.3.0-2025b.yml
@@ -2,3 +2,23 @@ easyconfigs:
   - Dyninst-13.0.0-GCC-14.3.0.eb
   - googletest-1.17.0-GCCcore-14.3.0.eb
   - SciPy-bundle-2025.07-gfbf-2025b.eb
+  - Pysam-0.23.3-GCC-14.3.0.eb
+  - Bowtie2-2.5.4-GCC-14.3.0.eb
+  - HMMER-3.4-gompi-2025b.eb
+  - MAFFT-7.526-GCC-14.3.0-with-extensions.eb
+  - GATK-4.6.2.0-GCCcore-14.3.0-Java-17.eb
+  - ViennaRNA-2.7.2-gfbf-2025b.eb
+  - ncbi-vdb-3.2.1-gompi-2025b.eb
+  - pyfaidx-0.9.0.3-GCCcore-14.3.0.eb
+  - SPAdes-4.2.0-GCC-14.3.0.eb
+  - pyBigWig-0.3.25-gfbf-2025b.eb
+  - fastp-1.1.0-GCC-14.3.0.eb
+  - AUGUSTUS-3.5.0-foss-2025b.eb
+  - SRA-Toolkit-3.2.1-gompi-2025b.eb
+  - BamTools-2.5.3-GCC-14.3.0.eb
+  - MMseqs2-18-8cc5c-gompi-2025b.eb
+  - PyHMMER-0.11.3-gompi-2025b.eb
+  - MEGAHIT-1.2.9-GCCcore-14.3.0.eb
+  - Racon-1.5.0-GCCcore-14.3.0.eb
+  - CD-HIT-4.8.1-GCC-14.3.0.eb
+  - Alfred-0.5.3-GCC-14.3.0.eb