Generating MiAIRR compliant GenBank/TLS submissions¶
The MiAIRR standard (minimal information about adaptive immune receptor repertoires) is a minimal reporting standard for experiments using sequencing-based technologies to study adaptive immune receptors (T and B cell receptors). The current version (1.0) of the standard was published in Rubelt et al, 2017 and accepted by the general assembly at the annual AIRR Community meeting in December 2017.
This example will cover generation of files for submission to TLS starting from Change-O formatted data. For complete details of the required and optional elements of the TLS submission see the AIRR Standards documentation site.
The following examples use the
S43_db-pass_parse-select.tab database file and
S43_template.sbt file provided in the example bundle, which has already undergone
the IgBLAST annotation, parsing, and filtering
Generating files for submission¶
- An annotated data set in either the Change-O or the AIRR Data Representation formats. Records must have valid V, J and junction region annotations to be suitable for submission.
- tbl2asn installed and in your
- A GenBank submission template file (
.sbt), generating using the NCBI Template Generator.
Cleaning up C-region annotations¶
First, we need to rename the C primer annotations to valid constant region gene names so they are
recognized by remote databases. We’ll use the update subcommand of
ParseDb to rename the values in the
CPRIMER column of the example file and save that
ParseDb.py update -d S43_db-pass_parse-select.tab -o S43_update.tab \ -f CPRIMER \ -u IgA-PCR IgD-PCR IgE-PCR IgG-PCR IgM-PCR \ -t IGHA IGHD IGHE IGHG IGHM
Creating ASN files¶
ASN submission files are generated using the genbank subcommand of ConvertDb as follows:
ConvertDb.py genbank -d S43_update.tab \ --product "immunoglobulin heavy chain" \ --db "IMGT/GENE-DB" \ --inf "IgBLAST:1.7.0" \ --organism "Homo sapiens" \ --tissue "Peripheral blood" \ --cell-type "B cell" \ --isolate S43 \ --cf CPRIMER \ --nf DUPCOUNT \ --asis-id \ --asn \ --sbt S43_template.sbt \ --outdir S43_TLS
The resulting output in the
S43_TLS folder will include a number of files.
The Sequin file
S43_update_genbank.sqn is the file that will be used for submission
and the GenBank record file
S43_update_genbank.gbf is similar to what the submission
will look like once it has been accepted by GenBank.
The command above manually specifies several required and optional annotations.
Alternatively, sample information (
cell_type) can be specified in a separate yaml file and provided via the
-y argument. Additional harmonized
which are not convered by the existing commandline arguments, may be provided
in the yaml file. Note, the yaml file adds only sample features, so it cannot be used
to specify source features (
--db arguments), parsing
arguments, or run parameters (–label`,
--exec, etc). Features specified in the yaml
file will override equivalent features specified through the corresponding commandline arguments.
The example shown above automatically runs tbl2asn, because the
--asn argument was specified. ConvertDb
can be run without running tbl2asn, which will generate only the
feature table (
S43_update_genbank.tbl) and fasta (
required to run tbl2asn manually via the command:
tbl2asn -p . -a s -V vb -t S43_template.sbt
There is a known issue with the
In some environments, for reasons that are presently unknown, tbl2asn
may fail to recongizing the input fasta file and report an error stating
Unable to read any FASTA records. Running tbl2asn manually should
resolve the issue.
Submitting to GenBank/TLS using SequinMacroSend¶
After generating the
.sqn files, you can submit them as MiAIRR compliant
GenBank/TLS records using GenBank’s
When submitting, simply add the keyword
AIRR to the subject line in the
submission system and it will be routed accordingly.
Currently, the SequinMacroSend system cannot accept files over 512MB in size.
For submissions over the size limit, you must split them into smaller files
and note in the submission comments that they are a part of a split submission.
.sqn files used for submission are usually about 30 times the size
of the original tab-delimited Change-O file. See the split subcommand
of ParseDb for one approach to logically dividing large submissions.