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Prepare a report for taxonomic assignment based on 16S rRNA sequences, using BLAST.
We're currently taking the sample ID from the input fasta filename:
Line 16 in d7e7c7c
...but when we use multi-fasta files, we want to take the ID from the fasta header.
It would be nice to include one or more 16S rRNA sequences in the repository to be used as testing examples when setting up the pipeline. This will streamline pipeline setup and Conda installation for users following the 16S SOP.
As a starting point, I will aim to add a single rRNA sequence with corresponding annotations to a new test
folder.
Allow the blast results to be filtered based on one or more regular expressions (regexes). This can be used to filter out 'uncultured' results, or other similar categories of results that are not wanted in the final blast output.
In order to flexibly support multiple regexes, they can be supplied in a multi-line file, with one line per regex. The file should be supplied using the --filter_regexes
flag, and it should be optional.
We've adopted a strategy for tracking database versioning and other metadata that involves storing a metadata.json
file alongside the blast database files.
At minimum, the metadata.json
file must include these fields:
{
"version": "1.1",
"date": "2020-06-24"
}
...though additional fields may be present (they will be ignored by this pipeline).
The version info will be included in each record of the blast results, under the fields:
database_version
database_date
In addition, the ID
field of the databases.csv
will be included under the field:
database_name
Database metadata should be collected by default, but it can be skipped using the --no_db_metadata
flag.
The pipeline is still labeled as BCCDC-PHL/fasta-blasta
We may want to blast against multiple databases, and aggregate the outputs into a single report.
To support an arbitrary number of databases, we could pass the databases as a samplesheet (dbsheet?) like this:
ID,DBNAME,PATH
ncbi_16S,16S_ribosomal_RNA,/path/to/ncbi/2023-09-19_1.1_16S_ribosomal_RNA
silva,SSURef_NR99_tax_silva_trunc,/path/to/silva/2020-08-24_138.1_SSURef_NR99_tax_silva_trunc
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