Comments (2)
For wort
I generated a name closer to GTBD:
GCF_000246355.1 Leptospira kirschneri serovar Mozdok str. 'B 81/7 type 3/Tsaratsovo' strain=B 81/7 type 3/Tsaratsovo, CLC_glsol0
I generate it from assembly_summary.txt
, using assembly_accession
, organism_name
, infraspecific_name
(if there is one) and finally a comma and asm_name
.
This example is pretty much the worst case I found: long name, with '
in the middle (so I need to escape properly in the shell). But the crucial point is using GCF_000246355.1
in the first position, because --name-from-first
in NCBI assemblies is a mess for our use cases.
from databases.
we've standardized over the last two years on putting the identifier first, as above, and we use this for pretty everything (including sourmash taxonomy
, and picklists). Everything seems to work fine ;). Closing as resolved 🎉 !
from databases.
Related Issues (10)
- upgrade sourmash_databases soon (for sourmash 4.0) HOT 8
- Validation steps for new databases HOT 1
- RefSeq representative genomes
- indexing from file (for sourmash 4.x)
- Please see other repositories and issues!
- 25k signatures HOT 3
- check genome_updater for genbank/refseq downloads HOT 8
- Building genbank/refseq databases from assembly_summary.txt HOT 1
- build a streamlined Genbank/RefSeq based on GTDB 25k genomes HOT 1
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from databases.