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This includes a stand-alone README and folder structure largely based on <https://github.com/nextstrain/zika/tree/a91e575bff38f154390c9eb11a44a89abf95a55b>
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# nextstrain.org/hbv/ingest | ||
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This is the ingest pipeline for Hepatitis B (HBV) virus sequences | ||
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## Software requirements | ||
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Follow the [standard installation instructions](https://docs.nextstrain.org/en/latest/install.html) for Nextstrain's suite of software tools. | ||
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## Usage | ||
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> NOTE: These command examples assume you are within the `ingest` directory. | ||
```sh | ||
snakemake --cores 4 | ||
``` | ||
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This produces a number of intermediate files in `data/` as well as three files in `results/` for downstream analysis: | ||
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- `results/metadata.tsv` | ||
- `results/sequences.fasta` | ||
- `results/aligned.fasta` | ||
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## Configuration | ||
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Configuration parameters are in `defaults/config.yaml`. These may be overridden by using Snakemake's `--configfile` or `--config` options. | ||
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### Environment Variables | ||
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None currently required | ||
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## Input data | ||
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### GenBank data | ||
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GenBank sequences and metadata are fetched via a NCBI Entrez query. | ||
As of mid 2024 there are around ~11.5k genomes and the full GenBank file is ~150Mb. | ||
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## `ingest/vendored` | ||
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This repository uses [`git subrepo`](https://github.com/ingydotnet/git-subrepo) to manage copies of ingest scripts in [ingest/vendored](./vendored), from [nextstrain/ingest](https://github.com/nextstrain/ingest). | ||
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See [vendored/README.md](vendored/README.md#vendoring) for instructions on how to update | ||
the vendored scripts. |
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# This configuration file should contain all required configuration parameters | ||
# for the ingest workflow to run to completion. | ||
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# Used to re-circularise genomes. This should be the same as the reference in the nextclade dataset! | ||
# Also force-included for a number of datasets | ||
reference_accession: "NC_003977" | ||
reference_genbank: "defaults/NC_003977.gb" | ||
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entrez_query: 'Hepatitis+B+virus[All+Fields]complete+genome[All+Fields]' | ||
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# Path to the nextclade dataset, which will be used to align all sequences | ||
nextclade_dataset: "../nextclade_datasets/references/NC_003977/versions/2023-08-22" | ||
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nextclade_binary: "../bin/nextclade" | ||
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# technically CDSs, but we use these terms rather interchangeably. | ||
# These should be the entire list of CDSs in the nextclade dataset's genemap | ||
genes: ['envS', 'envM', 'envL', 'X', 'pre-capsid', 'capsid', 'pol'] |
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