.

Author: DaanJansen94

README.md

@@ -146,6 +146,17 @@ Example HTML output for one sample:
 
 ![HTML Output Example](html_example.png)
 
+## Design and how Virasign works
+
+Virasign works in two steps: **(1)** map reads to a large viral DB (e.g. RVDB, RefSeq), **(2)** pick one best reference per viral species and remap all reads to that curated set.
+
+- **Best-reference selection**: References are deduplicated by viral species and one representative ref per species is chosen (by read count, identity, coverage), giving a small set of best refs instead of many near-duplicates.
+- **Why remap**: In one pass to the full DB, minimap2 reports one primary alignment per read, so the best ref “wins” and other species get no count. Remapping to the curated set gives correct counts per virus and meaningful BAM/FASTQ for consensus and downstream analysis, and increases specificity (fewer spurious hits).
+- **Why not secondary mapping**: Reporting multiple alignments per read in the first pass would create many false positives with a large DB and lower specificity. Virasign uses primary-only for the first pass, then deduplicates and remaps.
+- **Scale and flexibility**: Large viral DBs give sensitivity and completeness (e.g. catching more true viral hits, including low-abundance or divergent viruses). Custom databases and accessions are supported, and the tool is expandable to future reference sets.
+
+Also on [**Zenodo**](https://zenodo.org/records/18387009) and [**Docker**](https://hub.docker.com/repository/docker/daanjansen94/virasign/general).
+
 ## Citation
 
 If you use Virasign in your research, please cite:
@@ -164,15 +175,4 @@ Contributions are welcome! Please feel free to submit a Pull Request.
 
 ## Support
 
-If you encounter any problems or have questions, please open an issue on GitHub.
-
-## Design and how Virasign works
-
-Virasign works in two steps: **(1)** map reads to a large viral DB (e.g. RVDB, RefSeq), **(2)** pick one best reference per viral species and remap all reads to that curated set.
-
-- **Best-reference selection**: References are deduplicated by viral species and one representative ref per species is chosen (by read count, identity, coverage), giving a small set of best refs instead of many near-duplicates.
-- **Why remap**: In one pass to the full DB, minimap2 reports one primary alignment per read, so the best ref “wins” and other species get no count. Remapping to the curated set gives correct counts per virus and meaningful BAM/FASTQ for consensus and downstream analysis, and increases specificity (fewer spurious hits).
-- **Why not secondary mapping**: Reporting multiple alignments per read in the first pass would create many false positives with a large DB and lower specificity. Virasign uses primary-only for the first pass, then deduplicates and remaps.
-- **Scale and flexibility**: Large viral DBs give sensitivity and completeness (e.g. catching more true viral hits, including low-abundance or divergent viruses). Custom databases and accessions are supported, and the tool is expandable to future reference sets.
-
-Also on [**Zenodo**](https://zenodo.org/records/18387009) and [**Docker**](https://hub.docker.com/repository/docker/daanjansen94/virasign/general).
+If you encounter any problems or have questions, please open an issue on GitHub.