From b7e946618a064b1b57498ac87f65a525f407e195 Mon Sep 17 00:00:00 2001 From: asetGem <amandine.perrin@pasteur.fr> Date: Fri, 30 Jul 2021 15:28:49 +0200 Subject: [PATCH] add strain option to prepare module in doc --- doc/source/usage.rst | 1 + 1 file changed, 1 insertion(+) diff --git a/doc/source/usage.rst b/doc/source/usage.rst index 5c5ae0e1..8463f60a 100755 --- a/doc/source/usage.rst +++ b/doc/source/usage.rst @@ -211,6 +211,7 @@ Give at least one of ``-T``, ``-t`` or ``-g`` parameters (one of them is enough) - ``-g <NCBI species>``: the name of the species, as written by the NCBI. Give name between quotes. - ``-T <NCBI species taxid>``: the taxid provided by the NCBI for the species you want to download - ``-t <NCBI taxid>``: the taxid provided by the NCBI for the subspecies or specific strain you want to download +- ``-S <NCBI_strain>``: specific strain name you want to download. A comma-separated list of strain names is possible, as well as a file with 1 line per strain. If you want to download all genomes in genbank, and not only the ones in refseq, use option ``-s genbank`` (default is ``-s refseq``). -- GitLab