3 Methods
3.1 Data Submission
New users can contact the curators by e-mail (leptospiraMLST@pasteur.fr). Subsequently, the curators will create an account and
provide the log-in details to new users, who are then able to submit
their data (see Note 5). Whole-genome sequence data in FASTA
format can be submitted to BIGSdb as (1) a single contig of a
closed chromosome, (2) a multi-FASTA file with closed chromosome and plasmids from the same isolate, (3) multi-contig files
(whole-genome shotgun), or (4) scaffold files. There are a number
of fields that must be filled in so the curators know how the data
were obtained, e.g., the sequencing platform used, read length,
coverage, and assembly (de novo or mapped). Make sure the “email submission updates” box is checked if you wish to receive
e-mail notification of the result of your submission. Subsequently,
curators will check the quality of the data, and the sequences will be
automatically scanned for cgSTs and cgCGs assignments. cgSTs
represent profiles that differ by no allele other than for missing
data. cgSTs that share all but one or few alleles are considered to be
strongly related even if the differing alleles contain multiple singlenucleotide variants (SNVs) due to recombination. cgCGs are
defined by a single-linkage clustering threshold of 40 allelic mismatches; i.e., CG is defined as a group of cgMLST allelic profiles
differing by no more than 40 allelic mismatches, out of 545 gene
loci, from at least one other member of the group.
Every sequence entry should be accompanied by metadata of
the sample. The researchers are encouraged to upload as much
information about patients and isolates as available. The template
for Leptospira isolate metadata can be downloaded at the Institut
Pasteur MLST webpage (https://bigsdb.pasteur.fr/leptospira/).
Some fields are mandatory and cannot be left blank. Check the
“Description of database fields” link on the database contents page
to see a description of the fields and allowed values where these have
been defined.
3.2 Data Export
Different data can be exported from BIGSdb. You can export the
isolate recordsets by clicking the “Export dataset” link in the
Export section of the main contents page, or you can export
recordsets of isolates returned from a database query by clicking
the “Dataset” button in the Export list at the bottom of the results
table. You can then download the data in tab-delimited text or
Excel formats. In the advanced options, choose the cgMLST
scheme in order to export cgSTs and “Test-40” under the “Classification scheme” to obtain the cgCGs.
Similarly, the original submitted data as well as the sequences of
core genes extracted from the original data can be exported. By
default, the data will be extracted unaligned, but you can also
cgMLST Scheme for Leptospira
13
3.1 Data Submission
New users can contact the curators by e-mail (leptospiraMLST@pasteur.fr). Subsequently, the curators will create an account and
provide the log-in details to new users, who are then able to submit
their data (see Note 5). Whole-genome sequence data in FASTA
format can be submitted to BIGSdb as (1) a single contig of a
closed chromosome, (2) a multi-FASTA file with closed chromosome and plasmids from the same isolate, (3) multi-contig files
(whole-genome shotgun), or (4) scaffold files. There are a number
of fields that must be filled in so the curators know how the data
were obtained, e.g., the sequencing platform used, read length,
coverage, and assembly (de novo or mapped). Make sure the “email submission updates” box is checked if you wish to receive
e-mail notification of the result of your submission. Subsequently,
curators will check the quality of the data, and the sequences will be
automatically scanned for cgSTs and cgCGs assignments. cgSTs
represent profiles that differ by no allele other than for missing
data. cgSTs that share all but one or few alleles are considered to be
strongly related even if the differing alleles contain multiple singlenucleotide variants (SNVs) due to recombination. cgCGs are
defined by a single-linkage clustering threshold of 40 allelic mismatches; i.e., CG is defined as a group of cgMLST allelic profiles
differing by no more than 40 allelic mismatches, out of 545 gene
loci, from at least one other member of the group.
Every sequence entry should be accompanied by metadata of
the sample. The researchers are encouraged to upload as much
information about patients and isolates as available. The template
for Leptospira isolate metadata can be downloaded at the Institut
Pasteur MLST webpage (https://bigsdb.pasteur.fr/leptospira/).
Some fields are mandatory and cannot be left blank. Check the
“Description of database fields” link on the database contents page
to see a description of the fields and allowed values where these have
been defined.
3.2 Data Export
Different data can be exported from BIGSdb. You can export the
isolate recordsets by clicking the “Export dataset” link in the
Export section of the main contents page, or you can export
recordsets of isolates returned from a database query by clicking
the “Dataset” button in the Export list at the bottom of the results
table. You can then download the data in tab-delimited text or
Excel formats. In the advanced options, choose the cgMLST
scheme in order to export cgSTs and “Test-40” under the “Classification scheme” to obtain the cgCGs.
Similarly, the original submitted data as well as the sequences of
core genes extracted from the original data can be exported. By
default, the data will be extracted unaligned, but you can also
cgMLST Scheme for Leptospira
13