NARWHAL
NARWHAL — Neoantigens Recognition Website and HLA Genotyping Tool
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About NARWHAL
We developed a web interface to the NARWHAL, so users can easily submit DNA-seq/RNA-seq/LC-MASS files to the web server, select specific HLA types, and receive identified neoantigen candidates back by emails.
What can NARWHAL do?
NARWHAL is a comprehensive tool to identify putative neoantigens. This web-based toolkit can analyze various sample types (DNA-seq, RNA-seq, and LC-MS/MS data) which can identify both mTSAs and aeTSA with optimized steps. In addition, We also provide a web-based application to predict human leukocyte antigen (HLA) genotypes.
NARWHAL is published under the MIT license.
Copyright (c) 2024 Chia-Yu Sung and Chien-Yueh Lee
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
NARWHAL Update Information
| Version | Description |
|---|---|
| 202308 | Public release |
NARWHAL Example Data
| Data Type | Source | Download Link |
|---|---|---|
| RNA-seq | NCBI | Taiwanese colorectal cancer by using next-generation sequencing |
| DNA-seq | NCBI | Homo sapiens raw sequence reads |
List of Third-party Tools Incorporated into NARWHAL
| Tool Name | Version | Executing Function |
|---|---|---|
| arcasHLA | 0.4.0 | HLA genotyping |
| bedtools | 2.30.0 | File converter |
| Biopython | 1.68 | Tool development |
| BLAST | 2.9.0 | Local Alignment (merging with LC-MS/MS peptides) |
| BWA | 0.7.17 | Aligment (DNA) |
| covtobed | 1.2.0 | File converter |
| Dragmap | 1.2.1 | Aligment (DNA) |
| Ensembl-map | 1.2.0 | Gene annotation |
| Ensembl-vep | 104.3 | Gene annotation |
| Fastqc | 0.11.9 | Quality control, |
| GATK4 | 4.2.6 | Variant calling (DNA) |
| Jellyfish | 2.2.10 | k-mer profiling (aeTSA) |
| kallisto | 0.46.0 | Quantification of transcripts |
| MultiQC | 1.13 | Quality control, |
| Pandas | 1.3.5 | Tool development |
| Picard | 2.27.4 | MarkDuplicates |
| pip | 22.1.2 | Tool development |
| pVACtools | 3.1.0 | MHC binding affinity prediction |
| Pyensembl | 2.2.4 | k-mer profiling (aeTSA) |
| Python | 3.7 | Tool development |
| Samtools | 1.9 | VCF filtering |
| STAR | 2.7.10a | Aligment (RNA) |
| Trimmomatic | 0.39 | Adaptor trimming |
| unzip | 6 | Tool development |
| VarScan | 2.4.4 | Variant calling (RNA) |
List of Databases Incorporated into NARWHAL
| Database Name | Released Version/Date |
|---|---|
| COSMIC database | v98, 23rd May 2023 |
| Dragen reference | v8 |
| GRCh38 databases | 13rd Dec. 2017 |
| GRCh38.d1.vd1 Reference Sequence | md5: 3ffbcfe2d05d43206f57f81ebb251dc9 |
| IEDB databases | 3.1 |
| Illuminaclip | V0.32 |
| VEP cache | 104 |
| VEP plugins | 109 |