blastn
Tags: blast alignment nucleotide search fasta database sample-scope
Search a nucleotide database using nucleotide query sequences.
This subworkflow uses BLASTN to align nucleotide query sequences against a nucleotide BLAST database. It processes each sample individually and aggregates the alignment results into a single consolidated report for all samples.
Take
blastdb: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
blastdb | A compressed tarball containing the BLAST database |
query: Path
| Name | Type | Description |
|---|---|---|
query | Path | FASTA file containing nucleotide query sequences to search for in the assemblies |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
tsv | A tab-delimited summary of alignments (standard BLAST outfmt 6) |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- blast_blastn - Search a nucleotide database using a nucleotide query.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
Used By
This subworkflow is used by the following workflows:
- blastn - Search against nucleotide BLAST databases using nucleotide queries.
Citations
If you use this in your analysis, please cite the following.
-
Bactopia
Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020) -
BLAST
Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009)