Ale module

CHANGELOG.md

@@ -41,6 +41,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#873](https://github.com/nf-core/mag/pull/873) - Document usage of `longread_percentidentity` and `shortread_percentidentity` and set the value of `longread_percentidentity` in the `test_full` profile to 85 (by @prototaxites)
 - [#875](https://github.com/nf-core/mag/pull/875) - Add binner COMEBin (by @d4straub)
 
+- [#931](https://github.com/nf-core/mag/pull/931) - Added ALE (Assembly Likelihood Estimator) for probabilistic assembly quality control (by @PetcuBogdan)
+  - ALE provides per-contig quality scores for short-read assemblies (SPAdes, MEGAHIT)
+  - Runs automatically when binning is enabled (default behavior)
+  - Output: `Assembly/[assembler]/QC/[sample]/ALE/`
+  - Can be disabled with `--skip_ale` parameter
+
 ### `Changed`
 
 - [#878](https://github.com/nf-core/mag/pull/878) - Refine test_full config with optimised resource usage for AWS release megatests (by @jfy133)

assets/multiqc_config.yml

@@ -21,6 +21,7 @@ run_modules:
   - bowtie2
   - busco
   - quast
+  - ale
   - prokka
   - porechop
   - filtlong
@@ -55,6 +56,13 @@ top_modules:
       info: "Mapping statistics of reads mapped against host genome and subsequently removed."
       path_filters:
         - "*_host_removed.bowtie2.log"
+  - "ale":
+      name: "ALE: Assembly Likelihood Evaluation"
+      info: "Log-likelihood evaluation of assemblies using mapped reads (ALE module)."
+      path_filters:
+        - "*_ALE/*.ale"
+        - "*_ALE/*.txt"
+        - "*_ALE/*.log"
   - "quast":
       name: "QUAST: assembly"
       info: "Assembly statistics of raw assemblies."

conf/modules.config

@@ -407,6 +407,16 @@ process {
         publishDir = [path: { "${params.outdir}/Assembly/${meta.assembler}/QC/${meta.id}" }, mode: params.publish_dir_mode, saveAs: { filename -> filename.equals('versions.yml') ? null : filename }]
     }
 
+    withName: 'NFCORE_MAG:MAG:ALE' {
+        publishDir = [
+            path: { "${params.outdir}/Assembly/${meta.assembler?.toUpperCase() ?: 'UNKNOWN'}/QC/${meta.id}/ALE" },
+            mode: params.publish_dir_mode,
+            pattern: "*.{ale,txt,log}",
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+        ext.prefix = { "${meta.id}" }
+    }
+
     withName: 'QUAST_BINS|QUAST_BINS_SUMMARY' {
         publishDir = [
             path: { "${params.outdir}/GenomeBinning/QC" },

docs/output.md

@@ -300,6 +300,21 @@ SPAdesHybrid is a part of the [SPAdes](http://cab.spbu.ru/software/spades/) soft
 
 </details>
 
+### Assembly Quality Control with ALE
+
+[ALE (Assembly Likelihood Estimator)](https://github.com/sc932/ALE) is a probabilistic framework that evaluates assembly quality by computing the likelihood of the sequencing reads given an assembly. ALE provides per-contig quality scores and identifies potentially problematic regions in assemblies by analyzing read mapping patterns and insert size distributions. It is particularly useful for comparing assemblies and identifying misassemblies or low-confidence regions.
+
+ALE is run on short-read assemblies (SPAdes, SPAdes hybrid, and MEGAHIT) when binning or ancient DNA analysis is enabled.
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `Assembly/[assembler]/QC/[sample/group]/ALE/`
+  - `[sample]_ALEoutput.txt`: Per-contig ALE scores and quality metrics, including likelihood estimates for each contig
+  - `[sample].log`: ALE processing log file containing diagnostic information and runtime details
+
+</details>
+
 ## Gene prediction
 
 Protein-coding genes are predicted for each assembly.

docs/usage.md

@@ -454,6 +454,20 @@ This can also remove 'nonsense' bins of e.g. a single or a collection of very sh
 
 Note that in this context, it is recommended to also set `--min_length_unbinned_contigs` to a suitably high value that corresponds to a reasonable bin size if the `-bin_*_length` parameters are used, so you have useful 'singular' contigs in the unbinned output.
 
+## A note on assembly quality control with ALE
+
+The pipeline uses [ALE (Assembly Likelihood Estimator)](https://github.com/sc932/ALE) to perform probabilistic quality assessment of short-read assemblies generated by MEGAHIT and SPAdes.
+
+ALE evaluates assembly quality by computing the likelihood that the assembly could have generated the observed sequencing reads. Unlike traditional assembly QC tools that rely on reference genomes or marker genes, ALE provides a reference-free quality assessment that is particularly useful for novel organisms or complex metagenomes where references may not be available.
+
+ALE runs automatically when binning is enabled (default behavior), short reads are provided, and assemblies are generated with MEGAHIT or SPAdes. The tool generates quality assessment files in `Assembly/[assembler]/QC/[sample]/ALE/` containing per-assembly likelihood metrics (`[sample]_ALEoutput.txt`).
+
+ALE scores are log-likelihoods where higher (less negative) values indicate better assembly quality. These scores reflect how well the assembly explains the observed sequencing reads and can help identify assemblies that may have structural issues or errors that could affect downstream binning and annotation.
+
+If you wish to skip the ALE quality assessment step (for example, to speed up the pipeline when working with well-characterized samples), you can disable it with `--skip_ale`.
+
+Note that ALE only works with short-read assemblies (MEGAHIT, SPAdes). Long-read assemblies (Flye, MetaMDBG) are not supported by ALE, and hybrid assemblies (SPAdesHybrid) use only the short-read component for ALE scoring. For more information about ALE and how to interpret the results, see the [ALE GitHub repository](https://github.com/sc932/ALE) and the [publication](https://doi.org/10.1093/bioinformatics/bts723).
+
 ## A note on GTDB having too many files or using too many inodes
 
 The GTDB is very large both in size and by the number of files it contains.

modules.json

@@ -10,6 +10,11 @@
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
                         "installed_by": ["modules"]
                     },
+                    "ale": {
+                        "branch": "master",
+                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "installed_by": ["modules"]
+                    },
                     "bbmap/bbnorm": {
                         "branch": "master",
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",