Skip to content

Commit

Permalink
Merge pull request #248 from nextstrain/remove-inrb
Browse files Browse the repository at this point in the history
Remove `inrb.ndjson` as sequences now available via NCBI
  • Loading branch information
corneliusroemer authored May 6, 2024
2 parents d7a5581 + 4fabf67 commit 06dcb32
Show file tree
Hide file tree
Showing 2 changed files with 0 additions and 49 deletions.
47 changes: 0 additions & 47 deletions ingest/data/inrb.ndjson

This file was deleted.

2 changes: 0 additions & 2 deletions phylogenetic/defaults/description.md
Original file line number Diff line number Diff line change
Expand Up @@ -20,8 +20,6 @@ Our bioinformatic processing workflow can be found at [github.com/nextstrain/mpo
We curate sequence data and metadata from the [NCBI Datasets command line tools](https://www.ncbi.nlm.nih.gov/datasets/docs/v2/download-and-install/),
using an NCBI Taxonomy ID defined in [ingest/defaults/config.yaml](https://github.com/nextstrain/mpox/blob/master/ingest/defaults/config.yaml), as starting point for these analyses.

In addition to data shared via INSDC, we also include, with permission, sequences from INRB, the Institut National de Recherche Biomédicale in the Democratic Republic of the Congo, as shared via their Github repository [inrb-labgenpath/Mpox_sequencing_Kamituga](https://github.com/inrb-labgenpath/Mpox_sequencing_Kamituga). These sequences are discussed in the preprint [Sustained Human Outbreak of a New MPXV Clade I Lineage in Eastern Democratic Republic of the Congo](https://www.medrxiv.org/content/10.1101/2024.04.12.24305195v2).

Curated sequences and metadata are available as flat files at:
- [data.nextstrain.org/files/workflows/mpox/sequences.fasta.xz](https://data.nextstrain.org/files/workflows/mpox/sequences.fasta.xz)
- [data.nextstrain.org/files/workflows/mpox/metadata.tsv.gz](https://data.nextstrain.org/files/workflows/mpox/metadata.tsv.gz)
Expand Down

0 comments on commit 06dcb32

Please sign in to comment.