diff --git a/README.md b/README.md
index 2d15f73..037c9eb 100644
--- a/README.md
+++ b/README.md
@@ -221,7 +221,7 @@ SRR6180434,short_reads_filter_ratio_threshold_exceeded
 
 | Exclusion Message                 | Description                                                                                                                                                                                                                                                                            |
 | --------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `short_reads_filter_ratio_threshold_exceeded` | The maximum fraction of reads that are allowed to be filtered out. If exceeded, it flags excessive filtering. The default value is 0.9, meaning that if more than 90% of the reads are filtered out, the threshold is considered exceeded, and the run is not assembled. |
+| `short_reads_filter_ratio_threshold_exceeded` | The maximum fraction of reads that are allowed to be filtered out. If exceeded, it flags excessive filtering. The default value is 0.1, meaning that if less than 10% of the reads are retained after filtering, the threshold is considered exceeded, and the run is not assembled. |
 | `short_reads_low_reads_count_threshold`       | The minimum number of reads required after filtering. If below, it flags a low read count, and the run is not assembled.                                                                                                                                                               |
 
 #### Assembled Runs
diff --git a/nextflow.config b/nextflow.config
index e89c6d5..52f1cd3 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -32,7 +32,7 @@ params {
     // QC FILTERING
 
     // Short reads QC filtering options
-    short_reads_filter_ratio_threshold    = 0.9
+    short_reads_filter_ratio_threshold    = 0.1
     short_reads_low_reads_count_threshold = 1000
 
     // Long reads options
diff --git a/nextflow_schema.json b/nextflow_schema.json
index da9c14b..f3e69d7 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -194,8 +194,8 @@
             "properties": {
                 "short_reads_filter_ratio_threshold": {
                     "type": "number",
-                    "description": "The maximum fraction of reads that are allowed to be filtered out. If exceeded, it flags excessive filtering. The default value is 0.9, meaning that if more than 90% of the reads are filtered out, the threshold is considered exceeded, and the run is not assembled.",
-                    "default": 0.9,
+                    "description": "The maximum fraction of reads that are allowed to be filtered out. If exceeded, it flags excessive filtering. The default value is 0.1, meaning that if less than 10% of the reads are retained after filtering, the threshold is considered exceeded, and the run is not assembled.",
+                    "default": 0.1,
                     "minimum": 0.0,
                     "maximum": 1.0
                 },
diff --git a/workflows/short_reads_assembler.nf b/workflows/short_reads_assembler.nf
index f159e84..e38a676 100644
--- a/workflows/short_reads_assembler.nf
+++ b/workflows/short_reads_assembler.nf
@@ -94,7 +94,7 @@ workflow SHORT_READS_ASSEMBLER {
 
     /******************************************/
     /*  Reads that fail the following rules:  */
-    /*  - Reads discarded by fastp > 90% (default value) */
+    /*  - Reads kept by fastp < 10% (default value) */
     /*  - Less than 1k reads                  */
     /******************************************/
     extended_qc = SHORT_READS_QC.out.fastp_json.map { meta, json -> {