| Name | viralQC JSON |
| Version |
0.4.0
JSON |
| download |
| home_page | None |
| Summary | A tool and package for quality control of consensus virus genomes. |
| upload_time | 2025-10-11 13:08:19 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | <3.12,>=3.8 |
| license | MIT |
| keywords |
python
quality-control
snakemake
virus
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
## Install
ViralQC is a tool and package for quality control of consensus virus genomes which uses the [nextclade tool](https://docs.nextstrain.org/projects/nextclade/en/stable/), [BLAST](https://www.ncbi.nlm.nih.gov/books/NBK279690/) and a series of internal logics to classify viral sequences and perform quality control of complete genomes, regions or target genes.
### From pip
First, install the dependencies:
- [Snakemake 7.32](https://snakemake.readthedocs.io/en/v7.32.0/getting_started/installation.html)
- [Ncbi-blast 2.16](https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.16.0/)
- [Nextclade 3.15](https://docs.nextstrain.org/projects/nextclade/en/3.15.3/user/nextclade-cli/installation/)
- [Seqtk 1.5](https://github.com/lh3/seqtk/releases/tag/v1.5)
- [Python < 3.12](https://www.python.org/downloads/)
or with micromamba
```bash
micromamba install \
-c conda-forge \
-c bioconda \
"python>=3.8.0,<3.12.0" \
"snakemake-minimal>=7.32.0,<7.33.0" \
"blast>=2.16.0,<2.17.0" \
"nextclade>=3.15.0,<3.16.0" \
"seqtk>=1.5.0,<1.6.0"
```
Then, install viralQC
```bash
pip install viralQC
```
### From Source
```bash
git clone https://github.com/InstitutoTodosPelaSaude/viralQC.git
cd viralQC
```
#### Dependencies
```bash
micromamba env create -f env.yml
micromamba activate viralQC
```
#### viralQC
```bash
pip install .
```
### Check installation (CLI)
```bash
vqc --help
```
## Usage (CLI)
### get-nextclade-datasets
This command configures local datasets using nextclade. It is necessary to run at least once to generate a local copy of the nextclade datasets, before running the `run-from-fasta` command
```bash
vqc get-nextclade-datasets --cores 2
```
A directory name can be specified, the default is `datasets`.
```bash
vqc get-nextclade-datasets --cores 2 --datasets-dir <directory_name>
```
### get-blast-database
This command configures local blast database with all ncbi refseq viral genomes. It is necessary to run at least once to generate a local blast database, before running the `run-from-fasta` command.
```bash
vqc get-blast-database --cores 2
```
A output directory name can be specified, the default is `datasets`.
```bash
vqc get-nextclade-datasets --cores 2 --output-dir <directory_name>
```
### run-from-fasta
This command runs several steps to identify viruses represented in the input FASTA file and executes Nextclade for each identified virus/dataset.
#### run-from-fasta
```bash
vqc run-from-fasta --sequences-fasta test_data/sequences.fasta
```
Some parameters can be specified:
- `--output-dir` — Output directory name. **Default:** `output`
- `--output-file` - File to write final results. Valid extensions: .csv, .tsv or .json. **Default:** `results.tsv`
- `--datasets-dir` — Path to the local Nextclade datasets directory. **Default:** `datasets`
- `--ns-min-score` — Minimum score used by the Nextclade `sort` command. **Default:** `0.1`
- `--ns-min-hits` — Minimum number of hits for Nextclade to consider a dataset. **Default:** `10`
- `--blast-database` - Path to store local blast database. **Default:** `datasets/blast.fasta`
- `--identity-threshold` - Percentual identity threshold for BLAST analysis. **Default:** `0.9`
- `--cores` — Number of threads used in `nextclade sort` and `nextclade run`. **Default:** `1`
The output directory has the following structure:
```
├── <datasets> # Output from nextclade sort; sequences for each dataset split into sequences.fa files.
├── datasets_selected.tsv # Formatted nextclade sort output showing the mapping between input sequences and local datasets.
├── <virus/dataset>.nextclade.tsv # Nextclade run output for each identified virus, including clade assignments and QC metrics.
├── unmapped_sequences.txt # Names of input sequences that were not mapped to any virus on nextclade sort.
├── unmapped_sequences.blast.tsv # BLAST results for unmapped sequences.
└── viruses.tsv # Nextclade sort output showing the mapping between input sequences and remote
```
## Usage (API)
```bash
vqc-server
```
Go to `http://127.0.0.1:8000/docs`
### Development
Install development dependencies and run `black` into `viralqc` directory.
```bash
pip install -e ".[dev]"
black viralqc
```
Raw data
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"description": "## Install\n\nViralQC is a tool and package for quality control of consensus virus genomes which uses the [nextclade tool](https://docs.nextstrain.org/projects/nextclade/en/stable/), [BLAST](https://www.ncbi.nlm.nih.gov/books/NBK279690/) and a series of internal logics to classify viral sequences and perform quality control of complete genomes, regions or target genes.\n\n### From pip\n\nFirst, install the dependencies:\n\n- [Snakemake 7.32](https://snakemake.readthedocs.io/en/v7.32.0/getting_started/installation.html)\n- [Ncbi-blast 2.16](https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.16.0/)\n- [Nextclade 3.15](https://docs.nextstrain.org/projects/nextclade/en/3.15.3/user/nextclade-cli/installation/)\n- [Seqtk 1.5](https://github.com/lh3/seqtk/releases/tag/v1.5)\n- [Python < 3.12](https://www.python.org/downloads/)\n\nor with micromamba\n\n```bash\nmicromamba install \\\n -c conda-forge \\\n -c bioconda \\\n \"python>=3.8.0,<3.12.0\" \\\n \"snakemake-minimal>=7.32.0,<7.33.0\" \\\n \"blast>=2.16.0,<2.17.0\" \\\n \"nextclade>=3.15.0,<3.16.0\" \\\n \"seqtk>=1.5.0,<1.6.0\"\n```\n\nThen, install viralQC\n\n```bash\npip install viralQC\n```\n\n### From Source\n\n```bash\ngit clone https://github.com/InstitutoTodosPelaSaude/viralQC.git\ncd viralQC\n```\n\n#### Dependencies\n\n```bash\nmicromamba env create -f env.yml\nmicromamba activate viralQC\n```\n\n#### viralQC\n\n```bash\npip install .\n```\n\n### Check installation (CLI)\n\n```bash\nvqc --help\n```\n\n## Usage (CLI)\n\n### get-nextclade-datasets\n\nThis command configures local datasets using nextclade. It is necessary to run at least once to generate a local copy of the nextclade datasets, before running the `run-from-fasta` command\n\n```bash\nvqc get-nextclade-datasets --cores 2\n```\n\nA directory name can be specified, the default is `datasets`.\n\n```bash\nvqc get-nextclade-datasets --cores 2 --datasets-dir <directory_name>\n```\n\n### get-blast-database\n\nThis command configures local blast database with all ncbi refseq viral genomes. It is necessary to run at least once to generate a local blast database, before running the `run-from-fasta` command.\n\n```bash\nvqc get-blast-database --cores 2\n```\n\nA output directory name can be specified, the default is `datasets`.\n\n```bash\nvqc get-nextclade-datasets --cores 2 --output-dir <directory_name>\n```\n\n### run-from-fasta\n\nThis command runs several steps to identify viruses represented in the input FASTA file and executes Nextclade for each identified virus/dataset.\n\n#### run-from-fasta\n\n```bash\nvqc run-from-fasta --sequences-fasta test_data/sequences.fasta\n```\n\nSome parameters can be specified:\n\n- `--output-dir` \u2014 Output directory name. **Default:** `output`\n- `--output-file` - File to write final results. Valid extensions: .csv, .tsv or .json. **Default:** `results.tsv`\n- `--datasets-dir` \u2014 Path to the local Nextclade datasets directory. **Default:** `datasets`\n- `--ns-min-score` \u2014 Minimum score used by the Nextclade `sort` command. **Default:** `0.1`\n- `--ns-min-hits` \u2014 Minimum number of hits for Nextclade to consider a dataset. **Default:** `10`\n- `--blast-database` - Path to store local blast database. **Default:** `datasets/blast.fasta`\n- `--identity-threshold` - Percentual identity threshold for BLAST analysis. **Default:** `0.9`\n- `--cores` \u2014 Number of threads used in `nextclade sort` and `nextclade run`. **Default:** `1`\n\nThe output directory has the following structure:\n\n```\n\u251c\u2500\u2500 <datasets> # Output from nextclade sort; sequences for each dataset split into sequences.fa files.\n\u251c\u2500\u2500 datasets_selected.tsv # Formatted nextclade sort output showing the mapping between input sequences and local datasets.\n\u251c\u2500\u2500 <virus/dataset>.nextclade.tsv # Nextclade run output for each identified virus, including clade assignments and QC metrics.\n\u251c\u2500\u2500 unmapped_sequences.txt # Names of input sequences that were not mapped to any virus on nextclade sort.\n\u251c\u2500\u2500 unmapped_sequences.blast.tsv # BLAST results for unmapped sequences.\n\u2514\u2500\u2500 viruses.tsv # Nextclade sort output showing the mapping between input sequences and remote\n```\n\n## Usage (API)\n\n```bash\nvqc-server\n```\n\nGo to `http://127.0.0.1:8000/docs`\n\n### Development\n\nInstall development dependencies and run `black` into `viralqc` directory.\n\n```bash\npip install -e \".[dev]\"\nblack viralqc\n```\n",
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