Published May 5, 2025
| Version v1
Software
Open
Singularity containers for the OmniNeo workflow
Authors/Creators
- 1. Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200237, China.
- 2. Fudan Microbiome Center, State Key Laboratory of Genetic Engineering, Human Phenome Institute, and School of Life Sciences, Fudan University, Shanghai, 200438, China.
Description
Containers for the OmniNeo workflow publication: OmniNeo: A Multi-Omics Pipeline Incorporating Proteomics and AI Selection for Neoantigen Optimization in Tumor Immunotherapy
Details of software installed in the containers can be found below:
| category | function | software | version | container name |
| 1 | Quality control | fastp | 0.23.4 | fastp_0.23.4.sif |
| 2 | SAM/BAM manipulation | samtools | 1.3.1 | samtools_1.3.1--h60f3df9_12.sif |
| 3 | Read alignment | bwa | 0.7.19 | bwa_0.7.19--h577a1d6_0.sif |
| 4 | Variant calling and processing | gatk4 | 4.6.1.0 | gatk4_4.6.1.0--py310hdfd78af_0.sif |
| 5 | BAM file processing | picard | 3.4.0 | picard_3.4.0--hdfd78af_0.sif |
| 6 | RNA quantification | kallisto | 0.51.1 | kallisto_0.51.1--ha4fb952_1.sif |
| 7 | Proteomics analysis | maxquant | 2.0.3.0 | maxquant_2.0.3.0--py310hdfd78af_1.sif |
| 8 | Fusion detection | star-fusion | 1.14.0 | star-fusion_1.14.0--hdfd78af_2.sif |
| 9 | HLA Class I typing | optitype | 1.3.3 | optitype_latest.sif |
| 10 | VCF manipulation | bcftools | 1.21 | bcftools_1.21--h3a4d415_1.sif |
| 11 | downstream analysis | Python | 3.6 | python_3.6_bio.sif |
| 12 | AI Selection for Neoantigen Optimization | Pytorch | 2.7.0 | pytorch_latest.sif |
Files
Files
(10.0 GB)
| Name | Size | Download all |
|---|---|---|
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md5:558686e12910e1a59a2c458580637d6a
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63.5 MB | Download |
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md5:912b816d209d2ca8d87ed94739bac641
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25.4 MB | Download |
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md5:ee1d3ff2b9b92c8f1ca255fabb87c358
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14.5 MB | Download |
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md5:f5013d139c1a534f9feadeb65439bfe0
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716.6 MB | Download |
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md5:f5df4ac4ac5bc7872b04a88fa62a986e
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29.2 MB | Download |
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md5:82dee4389010dbd3408a2a12f226e1f2
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626.0 MB | Download |
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md5:1e4e17dd9fdc6738f4b20c9913bcb2e2
|
557.4 MB | Download |
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md5:90da6016f5b1d31bf72fddf5fb6e44ef
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619.9 MB | Download |
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md5:eb89f83e4143180d8bfa88b03dac2daa
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83.8 MB | Download |
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md5:aea3f2c1048ea8bcd99d19cc46929386
|
6.5 GB | Download |
|
md5:d99ec6438ed2bc16413cdd58f815d06a
|
21.7 MB | Download |
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md5:93d73fc053bb3d3677eb384c666fcbc4
|
738.1 MB | Download |
Additional details
Software
- Repository URL
- https://github.com/linfengxu/OmniNeo