Linking remote contigs to isolate records
If remote contigs have been enabled, isolates
can be linked to contigs stored in an external BIGSdb database, rather than
directly uploaded. These well then be loaded when needed, for example during
scanning or data export. This will be marginally slower than hosting contigs
within the same database, but minimises duplication of sequence data and
associated storage. Contigs need to be accessible via the BIGSdb
Click the sequences link icon on the curator’s main page.
Either select the isolate id from the dropdown list, or enter it manually
(list is disabled if there are >1000 records in the database). Enter the URI
for the RESTful API of the parent isolate record, e.g.
http://rest.pubmlst.org/db/pubmlst_rmlst_isolates/isolates/933. This URI can
require authentication if credentials have been
Summary information about the number of contigs and their total length will
be downloaded from the remote isolate record. You will then be prompted to
upload this information to the database, by clicking the ‘Upload’ button.
The contigs will be downloaded in bulk in order to determine their lengths.
This information is stored within the local database as it is required for
various outputs. Full metadata is not stored at this stage.
This is all that is required for the contigs to be used as normal. In order
to get the full metadata about the contigs (sequencing platform used, sender
and datestamp information), you can choose to process the contigs by clicking
the ‘Process contigs now’ button. This will download each contig in turn, and
store its provenance metadata locally.
Alternatively, this step can be
performed offline automatically.