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[MRG] Update DB links in docs #1084

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merged 5 commits into from
Jul 14, 2020
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[MRG] Update DB links in docs #1084

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737a556
use zipped databases
luizirber Jul 7, 2020
2ba0bb8
fix numbers
luizirber Jul 7, 2020
dc29e05
use OSF links
luizirber Jul 7, 2020
4824cd4
Merge branch 'master' of github.com:dib-lab/sourmash into doc/new_zip…
ctb Jul 14, 2020
bc1d1b9
add manifest links
ctb Jul 14, 2020
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28 changes: 14 additions & 14 deletions doc/databases.md
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Expand Up @@ -5,24 +5,24 @@
These database are formatted for use with `sourmash search` and
`sourmash gather`. They are calculated with a scaled value of 2000.

Approximately 60,000 microbial genomes (including viral and fungal)
Approximately 91,000 microbial genomes (including viral and fungal)
from NCBI RefSeq.

* [RefSeq k=21, 2018.03.29][0] - 7 GB
* [RefSeq k=31, 2018.03.29][1] - 7 GB
* [RefSeq k=51, 2018.03.29][2] - 7.1 GB
* [RefSeq k=21, 2018.03.29][0] - 3.3 GB - [manifest](https://osf.io/wamfk/download)
* [RefSeq k=31, 2018.03.29][1] - 3.3 GB - [manifest](https://osf.io/x3aut/download)
* [RefSeq k=51, 2018.03.29][2] - 3.4 GB - [manifest](https://osf.io/zpkau/download)

## Genbank microbial genomes - SBT

These database are formatted for use with `sourmash search` and
`sourmash gather`.

Approximately 100,000 microbial genomes (including viral and fungal)
Approximately 98,000 microbial genomes (including viral and fungal)
from NCBI Genbank.

* [Genbank k=21, 2018.03.29][3]- 8.4 GB
* [Genbank k=31, 2018.03.29][4] - 8.4 GB
* [Genbank k=51, 2018.03.29][5] - 8.4 GB
* [Genbank k=21, 2018.03.29][3] - 3.9 GB - [manifest](https://osf.io/vm5kb/download)
* [Genbank k=31, 2018.03.29][4] - 3.9 GB - [manifest](https://osf.io/p87ec/download)
* [Genbank k=51, 2018.03.29][5] - 3.9 GB - [manifest](https://osf.io/cbxg9/download)

### Details

Expand All @@ -47,12 +47,12 @@ sourmash compute -k 21,31,51 \
See [github.com/dib-lab/sourmash_databases](https://github.com/dib-lab/sourmash_databases) for a Snakemake workflow
to build the databases.

[0]: https://s3-us-west-2.amazonaws.com/sourmash-databases/2018-03-29/refseq-d2-k21.tar.gz
[1]: https://s3-us-west-2.amazonaws.com/sourmash-databases/2018-03-29/refseq-d2-k31.tar.gz
[2]: https://s3-us-west-2.amazonaws.com/sourmash-databases/2018-03-29/refseq-d2-k51.tar.gz
[3]: https://s3-us-west-2.amazonaws.com/sourmash-databases/2018-03-29/genbank-d2-k21.tar.gz
[4]: https://s3-us-west-2.amazonaws.com/sourmash-databases/2018-03-29/genbank-d2-k31.tar.gz
[5]: https://s3-us-west-2.amazonaws.com/sourmash-databases/2018-03-29/genbank-d2-k51.tar.gz
[0]: https://osf.io/k26ep/download
[1]: https://osf.io/8snc9/download
[2]: https://osf.io/gkqau/download
[3]: https://osf.io/dm7n4/download
[4]: https://osf.io/jgu93/download
[5]: https://osf.io/2uvsc/download

## Genbank LCA Database

Expand Down