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update nextclade datasets #1378

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update nextclade datasets #1378

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24bb09f
update nextclade datasets
Joon-Klaps Nov 5, 2024
8f3895d
update readme
Joon-Klaps Nov 5, 2024
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62 changes: 32 additions & 30 deletions README.md
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Expand Up @@ -49,56 +49,58 @@ kraken2-build --db kraken2_hs22 --build

#### `NC_045512.2/`

* `GCF_009858895.2_ASM985889v3_genomic.<DOWNLOAD_DATE>.fna.gz`: SARS-CoV2 genome fasta file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/858/895/GCF_009858895.2_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna.gz)
* `GCF_009858895.2_ASM985889v3_genomic.<DOWNLOAD_DATE>.gff.gz`: SARS-CoV2 genome GFF3 annotation file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/858/895/GCF_009858895.2_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.gff.gz)
* `GCF_009858895.2_ASM985889v3_genomic.<DOWNLOAD_DATE>.gtf.gz`: SARS-CoV2 genome GTF2.2 annotation file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/858/895/GCF_009858895.2_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.gtf.gz)
* `amplicon/`: ARTIC [V1](https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V1), [V2](https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V2) and [V3](https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V3) primer schema files relative to the NC_045512.2 assembly. Files ending in `*.primer.fasta` were generated from the `.tsv` files in the repo.
- `GCF_009858895.2_ASM985889v3_genomic.<DOWNLOAD_DATE>.fna.gz`: SARS-CoV2 genome fasta file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/858/895/GCF_009858895.2_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.fna.gz)
- `GCF_009858895.2_ASM985889v3_genomic.<DOWNLOAD_DATE>.gff.gz`: SARS-CoV2 genome GFF3 annotation file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/858/895/GCF_009858895.2_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.gff.gz)
- `GCF_009858895.2_ASM985889v3_genomic.<DOWNLOAD_DATE>.gtf.gz`: SARS-CoV2 genome GTF2.2 annotation file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/858/895/GCF_009858895.2_ASM985889v3/GCF_009858895.2_ASM985889v3_genomic.gtf.gz)
- `amplicon/`: ARTIC [V1](https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V1), [V2](https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V2) and [V3](https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V3) primer schema files relative to the NC_045512.2 assembly. Files ending in `*.primer.fasta` were generated from the `.tsv` files in the repo.

#### `MN908947.3/`

* `GCA_009858895.3_ASM985889v3_genomic.<DOWNLOAD_DATE>.fna.gz`: SARS-CoV2 genome fasta file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3/GCA_009858895.3_ASM985889v3_genomic.fna.gz)
* `GCA_009858895.3_ASM985889v3_genomic.<DOWNLOAD_DATE>.gff.gz`: SARS-CoV2 genome GFF3 annotation file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3/GCA_009858895.3_ASM985889v3_genomic.gff.gz)
* `GCA_009858895.3_ASM985889v3_genomic.<DOWNLOAD_DATE>.gtf.gz`: SARS-CoV2 genome GTF2.2 annotation file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3/GCA_009858895.3_ASM985889v3_genomic.gtf.gz)
* `amplicon/`: ARTIC [V1](https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V1), [V2](https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V2) and [V3](https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V3) primer schema files relative to the MN908947.3 assembly. Files ending in `*.primer.fasta` were generated from the `.tsv` files in the repo.
- `GCA_009858895.3_ASM985889v3_genomic.<DOWNLOAD_DATE>.fna.gz`: SARS-CoV2 genome fasta file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3/GCA_009858895.3_ASM985889v3_genomic.fna.gz)
- `GCA_009858895.3_ASM985889v3_genomic.<DOWNLOAD_DATE>.gff.gz`: SARS-CoV2 genome GFF3 annotation file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3/GCA_009858895.3_ASM985889v3_genomic.gff.gz)
- `GCA_009858895.3_ASM985889v3_genomic.<DOWNLOAD_DATE>.gtf.gz`: SARS-CoV2 genome GTF2.2 annotation file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/009/858/895/GCA_009858895.3_ASM985889v3/GCA_009858895.3_ASM985889v3_genomic.gtf.gz)
- `amplicon/`: ARTIC [V1](https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V1), [V2](https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V2) and [V3](https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V3) primer schema files relative to the MN908947.3 assembly. Files ending in `*.primer.fasta` were generated from the `.tsv` files in the repo.
- `nextclade_sars-cov-2_MN908947_2024-10-17--16_48_48Z.tar.gz`: A set of input data files required for Nextclade to run an analysis on SARS-CoV2. Previous format did not require `pathogen.json` file but from v3+ it is required. File was created with `nextclade dataset get -n sars-cov-2 --tag 2024-10-17--16-48-48Z`.

#### `NC_063383.1`

* `GCF_014621545.1_ASM1462154v1_genomic.<DOWNLOAD_DATE>.fna.gz`: Monkeypox genome fasta file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/621/545/GCF_014621545.1_ASM1462154v1/GCF_014621545.1_ASM1462154v1_genomic.fna.gz)
* `GCF_014621545.1_ASM1462154v1_genomic.<DOWNLOAD_DATE>.gff.gz`: Monkeypox genome GFF3 annotation file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/621/545/GCF_014621545.1_ASM1462154v1/GCF_014621545.1_ASM1462154v1_genomic.gff.gz)
- `GCF_014621545.1_ASM1462154v1_genomic.<DOWNLOAD_DATE>.fna.gz`: Monkeypox genome fasta file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/621/545/GCF_014621545.1_ASM1462154v1/GCF_014621545.1_ASM1462154v1_genomic.fna.gz)
- `GCF_014621545.1_ASM1462154v1_genomic.<DOWNLOAD_DATE>.gff.gz`: Monkeypox genome GFF3 annotation file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/014/621/545/GCF_014621545.1_ASM1462154v1/GCF_014621545.1_ASM1462154v1_genomic.gff.gz)
- `nextclade_hMPXV_NC_063383.1_2024-08-27--21-28-04Z.tar.gz`: A set of input data files required for Nextclade to run an analysis on MPOX. Previous format did not require `pathogen.json` file but from v3+ it is required. File was created with `nextclade dataset get -n MPXV --tag 2024-08-27--21-28-04Z`.
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@jfy133 jfy133 Nov 5, 2024 •
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Is the previous version lsited somewhere 🤔 ?

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No it wasn't


#### `ON563414.3`

* `GCA_023516015.3_ASM2351601v1_genomic.<DOWNLOAD_DATE>.fna.gz`: Monkeypox genome fasta file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/023/516/015/GCA_023516015.3_ASM2351601v1/GCA_023516015.3_ASM2351601v1_genomic.fna.gz)
* `GCA_023516015.3_ASM2351601v1_genomic.<DOWNLOAD_DATE>.gff.gz`: Monkeypox genome GFF3 annotation file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/023/516/015/GCA_023516015.3_ASM2351601v1/GCA_023516015.3_ASM2351601v1_genomic.gff.gz)
- `GCA_023516015.3_ASM2351601v1_genomic.<DOWNLOAD_DATE>.fna.gz`: Monkeypox genome fasta file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/023/516/015/GCA_023516015.3_ASM2351601v1/GCA_023516015.3_ASM2351601v1_genomic.fna.gz)
- `GCA_023516015.3_ASM2351601v1_genomic.<DOWNLOAD_DATE>.gff.gz`: Monkeypox genome GFF3 annotation file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/023/516/015/GCA_023516015.3_ASM2351601v1/GCA_023516015.3_ASM2351601v1_genomic.gff.gz)

#### `MT903344.1`

* `GCA_014621585.1_ASM1462158v1_genomic.<DOWNLOAD_DATE>.fna.gz`: Monkeypox genome fasta file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/621/585/GCA_014621585.1_ASM1462158v1/GCA_014621585.1_ASM1462158v1_genomic.fna.gz)
* `GCA_014621585.1_ASM1462158v1_genomic.<DOWNLOAD_DATE>.gff.gz`: Monkeypox genome GFF3 annotation file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/621/585/GCA_014621585.1_ASM1462158v1/GCA_014621585.1_ASM1462158v1_genomic.gff.gz)
- `GCA_014621585.1_ASM1462158v1_genomic.<DOWNLOAD_DATE>.fna.gz`: Monkeypox genome fasta file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/621/585/GCA_014621585.1_ASM1462158v1/GCA_014621585.1_ASM1462158v1_genomic.fna.gz)
- `GCA_014621585.1_ASM1462158v1_genomic.<DOWNLOAD_DATE>.gff.gz`: Monkeypox genome GFF3 annotation file downloaded directly via [NCBI FTP](https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/014/621/585/GCA_014621585.1_ASM1462158v1/GCA_014621585.1_ASM1462158v1_genomic.gff.gz)

### `fastq/illumina_sispa/`

| file | num_seqs | sum_len | min_len | avg_len | max_len | file_size | Sequencer | LibrarySource |
|-------------------------|----------|------------|---------|---------|---------|-----------|-------------|--------------------|
| SRR11140744_R1.fastq.gz | 10,092 | 2,284,737 | 100 | 175.5 | 251 | 747K | PE Illumina | Metagenomics |
| SRR11140744_R2.fastq.gz | 10,092 | 2,260,970 | 100 | 175.5 | 251 | 783K | PE Illumina | Metagenomics |
| SRR11140746_R1.fastq.gz | 7,196 | 1,609,884 | 100 | 175.5 | 251 | 554K | PE Illumina | Metagenomics |
| SRR11140746_R2.fastq.gz | 7,196 | 1,594,703 | 100 | 175.5 | 251 | 580K | PE Illumina | Metagenomics |
| SRR11140748_R1.fastq.gz | 8,447 | 1,918,541 | 100 | 175.5 | 251 | 650K | PE Illumina | Metagenomics |
| SRR11140748_R2.fastq.gz | 8,447 | 1,903,781 | 100 | 175.5 | 251 | 683K | PE Illumina | Metagenomics |
| SRR11140750_R1.fastq.gz | 369 | 81,898 | 100 | 175.5 | 251 | 40K | PE Illumina | Metagenomics |
| SRR11140750_R2.fastq.gz | 369 | 80,344 | 102 | 176.5 | 251 | 41K | PE Illumina | Metagenomics |
| file | num_seqs | sum_len | min_len | avg_len | max_len | file_size | Sequencer | LibrarySource |
| ----------------------- | -------- | --------- | ------- | ------- | ------- | --------- | ----------- | ------------- |
| SRR11140744_R1.fastq.gz | 10,092 | 2,284,737 | 100 | 175.5 | 251 | 747K | PE Illumina | Metagenomics |
| SRR11140744_R2.fastq.gz | 10,092 | 2,260,970 | 100 | 175.5 | 251 | 783K | PE Illumina | Metagenomics |
| SRR11140746_R1.fastq.gz | 7,196 | 1,609,884 | 100 | 175.5 | 251 | 554K | PE Illumina | Metagenomics |
| SRR11140746_R2.fastq.gz | 7,196 | 1,594,703 | 100 | 175.5 | 251 | 580K | PE Illumina | Metagenomics |
| SRR11140748_R1.fastq.gz | 8,447 | 1,918,541 | 100 | 175.5 | 251 | 650K | PE Illumina | Metagenomics |
| SRR11140748_R2.fastq.gz | 8,447 | 1,903,781 | 100 | 175.5 | 251 | 683K | PE Illumina | Metagenomics |
| SRR11140750_R1.fastq.gz | 369 | 81,898 | 100 | 175.5 | 251 | 40K | PE Illumina | Metagenomics |
| SRR11140750_R2.fastq.gz | 369 | 80,344 | 102 | 176.5 | 251 | 41K | PE Illumina | Metagenomics |

> All FastQ files were sub-sampled to 0.02% of the original reads.

### `fastq/illumina_amplicon/`

| file | num_seqs | sum_len | min_len | avg_len | max_len | file_size | Sequencer | LibrarySource |
|-------------------------|----------|------------|---------|---------|---------|-----------|-------------|--------------------|
| sample1_R1.fastq.gz | 27,721 | 8,285,732 | 35 | 168 | 301 | 4M | PE Illumina | Metagenomics |
| sample1_R2.fastq.gz | 27,721 | 8,285,900 | 35 | 168 | 301 | 4M | PE Illumina | Metagenomics |
| sample2_R1.fastq.gz | 21,481 | 6,416,734 | 35 | 168 | 301 | 3M | PE Illumina | Metagenomics |
| sample2_R2.fastq.gz | 21,481 | 6,416,265 | 35 | 168 | 301 | 3M | PE Illumina | Metagenomics |
| file | num_seqs | sum_len | min_len | avg_len | max_len | file_size | Sequencer | LibrarySource |
| ------------------- | -------- | --------- | ------- | ------- | ------- | --------- | ----------- | ------------- |
| sample1_R1.fastq.gz | 27,721 | 8,285,732 | 35 | 168 | 301 | 4M | PE Illumina | Metagenomics |
| sample1_R2.fastq.gz | 27,721 | 8,285,900 | 35 | 168 | 301 | 4M | PE Illumina | Metagenomics |
| sample2_R1.fastq.gz | 21,481 | 6,416,734 | 35 | 168 | 301 | 3M | PE Illumina | Metagenomics |
| sample2_R2.fastq.gz | 21,481 | 6,416,265 | 35 | 168 | 301 | 3M | PE Illumina | Metagenomics |

> All FastQ files were sub-sampled to 0.02% of the original reads.

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