diff --git a/CHANGELOG.md b/CHANGELOG.md
index c5d7c7b9..0557ad5b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -19,9 +19,13 @@ The pipeline is now considered to be a complete and suitable replacement for the
 
 Note, since the pipeline is using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference. Only `Docker` or `Singularity` containers are supported, `conda` is not supported.
 
-| Dependency  | Old version | New version |
-| ----------- | ----------- | ----------- |
-| blobtoolkit | 4.3.9       | 4.3.13      |
+| Dependency  | Old version       | New version     |
+| ----------- | ----------------- | --------------- |
+| blast       | 2.14.1 and 2.15.0 | only 2.15.0     |
+| blobtoolkit | 4.3.9             | 4.4.0           |
+| busco       | 5.5.0             | 5.7.1           |
+| multiqc     | 1.20 and 1.21     | 1.20 and 1.25.1 |
+| samtools    | 1.18 and 1.19.2   | 1.20 and 1.21   |
 
 ## [[0.6.0](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.6.0)] – Bellsprout – [2024-09-13]
 
@@ -112,7 +116,7 @@ Note, since the pipeline is using Nextflow DSL2, each process will be run with i
 | blobtoolkit | 4.3.3         | 4.3.9             |
 | blast       | 2.14.0        | 2.15.0 and 2.14.1 |
 | multiqc     | 1.17 and 1.18 | 1.20 and 1.21     |
-| samtools    | 1.18          | 1.19.2            |
+| samtools    | 1.18          | 1.18 and 1.19.2   |
 | seqtk       | 1.3           | 1.4               |
 
 > **NB:** Dependency has been **updated** if both old and new version information is present. </br> **NB:** Dependency has been **added** if just the new version information is present. </br> **NB:** Dependency has been **removed** if version information isn't present.
diff --git a/docs/usage.md b/docs/usage.md
index 6f8909bf..8fe227b7 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -272,7 +272,7 @@ List of tools for any given dataset can be fetched from the API, for example htt
 
 | Dependency        | Snakemake | Nextflow |
 | ----------------- | --------- | -------- |
-| blobtoolkit       | 4.3.2     | 4.3.13   |
+| blobtoolkit       | 4.3.2     | 4.4.0   |
 | blast             | 2.12.0    | 2.14.1   |
 | blobtk            | 0.5.0     | 0.5.1    |
 | busco             | 5.3.2     | 5.5.0    |
diff --git a/modules/local/blobtoolkit/chunk.nf b/modules/local/blobtoolkit/chunk.nf
index 0b8a7989..80deca41 100644
--- a/modules/local/blobtoolkit/chunk.nf
+++ b/modules/local/blobtoolkit/chunk.nf
@@ -5,7 +5,7 @@ process BLOBTOOLKIT_CHUNK {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_CHUNK module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta) , path(fasta)
diff --git a/modules/local/blobtoolkit/countbuscos.nf b/modules/local/blobtoolkit/countbuscos.nf
index 0e525ede..5cc9e37f 100644
--- a/modules/local/blobtoolkit/countbuscos.nf
+++ b/modules/local/blobtoolkit/countbuscos.nf
@@ -5,7 +5,7 @@ process BLOBTOOLKIT_COUNTBUSCOS {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_COUNTBUSCOS module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(table, stageAs: 'dir??/*')
diff --git a/modules/local/blobtoolkit/createblobdir.nf b/modules/local/blobtoolkit/createblobdir.nf
index b68e32a1..487dfee3 100644
--- a/modules/local/blobtoolkit/createblobdir.nf
+++ b/modules/local/blobtoolkit/createblobdir.nf
@@ -5,7 +5,7 @@ process BLOBTOOLKIT_CREATEBLOBDIR {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_BLOBDIR module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(window, stageAs: 'windowstats/*')
diff --git a/modules/local/blobtoolkit/extractbuscos.nf b/modules/local/blobtoolkit/extractbuscos.nf
index bd598539..c8346211 100644
--- a/modules/local/blobtoolkit/extractbuscos.nf
+++ b/modules/local/blobtoolkit/extractbuscos.nf
@@ -5,7 +5,7 @@ process BLOBTOOLKIT_EXTRACTBUSCOS {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_EXTRACTBUSCOS module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(fasta)
diff --git a/modules/local/blobtoolkit/summary.nf b/modules/local/blobtoolkit/summary.nf
index 539fe9c8..e1736d67 100644
--- a/modules/local/blobtoolkit/summary.nf
+++ b/modules/local/blobtoolkit/summary.nf
@@ -5,7 +5,7 @@ process BLOBTOOLKIT_SUMMARY {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_SUMMARY module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(blobdir)
diff --git a/modules/local/blobtoolkit/unchunk.nf b/modules/local/blobtoolkit/unchunk.nf
index 87fa1bb5..99060a6b 100644
--- a/modules/local/blobtoolkit/unchunk.nf
+++ b/modules/local/blobtoolkit/unchunk.nf
@@ -5,7 +5,7 @@ process BLOBTOOLKIT_UNCHUNK {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_UNCHUNK module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(blast_table)
diff --git a/modules/local/blobtoolkit/updateblobdir.nf b/modules/local/blobtoolkit/updateblobdir.nf
index b3940642..f6bafae7 100644
--- a/modules/local/blobtoolkit/updateblobdir.nf
+++ b/modules/local/blobtoolkit/updateblobdir.nf
@@ -5,7 +5,7 @@ process BLOBTOOLKIT_UPDATEBLOBDIR {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_BLOBDIR module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(input, stageAs: "input_blobdir")
diff --git a/modules/local/blobtoolkit/updatemeta.nf b/modules/local/blobtoolkit/updatemeta.nf
index 356e6699..de664149 100644
--- a/modules/local/blobtoolkit/updatemeta.nf
+++ b/modules/local/blobtoolkit/updatemeta.nf
@@ -5,7 +5,7 @@ process BLOBTOOLKIT_UPDATEMETA {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_UPDATEMETA module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(input)
diff --git a/modules/local/blobtoolkit/windowstats.nf b/modules/local/blobtoolkit/windowstats.nf
index 7ca59db4..e6445f6b 100644
--- a/modules/local/blobtoolkit/windowstats.nf
+++ b/modules/local/blobtoolkit/windowstats.nf
@@ -4,7 +4,7 @@ process BLOBTOOLKIT_WINDOWSTATS {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         exit 1, "BLOBTOOLKIT_WINDOWSTATS module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), path(tsv)
diff --git a/modules/local/generate_config.nf b/modules/local/generate_config.nf
index 12097381..d4200641 100644
--- a/modules/local/generate_config.nf
+++ b/modules/local/generate_config.nf
@@ -3,7 +3,7 @@ process GENERATE_CONFIG {
     label 'process_single'
 
     conda "conda-forge::requests=2.28.1 conda-forge::pyyaml=6.0"
-    container "docker.io/genomehubs/blobtoolkit:4.3.13"
+    container "docker.io/genomehubs/blobtoolkit:4.4.0"
 
     input:
     tuple val(meta), val(fasta)