blast_tblastn

Tags: blast tblastn alignment translation protein dna search fasta sample-scope

Search a translated nucleotide database using a protein query.

Uses TBLASTN to align amino acid query sequences (FASTA) against a nucleotide BLAST database that has been dynamically translated in all six reading frames. This is useful for finding gene homologs in unannotated genomic DNA.

Inputs

record (
    meta: Record,
    blastdb: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
blastdb	Path	A compressed tarball containing the nucleotide BLAST database

query: Path

Name	Type	Description
query	Path	FASTA file containing amino acid query sequences

Outputs

record (
    meta: Record,
    tsv: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	Tab-delimited protein-to-translated nucleotide alignment results (BLAST outfmt 6)
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

TBLASTN Parameters

Parameter	Type	Default	Description
--tblastn_query	string		A fasta file containing the query sequences to BLAST against the database
--tblastn_outfmt	string	sseqid qseqid pident qlen slen length nident positive mismatch gapopen gaps qstart qend sstart send evalue bitscore	The columns to include with -outfmt 6
--tblastn_opts	string		Additional options to pass to BLASTN
--tblastn_qcov_hsp_perc	integer	50	Percent query coverage per hsp
--tblastn_max_target_seqs	integer	2000	Maximum number of aligned sequences to keep

Used By

Subworkflows

• tblastn - Search protein query sequences against nucleotide database.

Workflows

• tblastn - Search against translated nucleotide databases using protein 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)

Source

View source on GitHub

Version

BLAST_TBLASTN:
    - blast: 2.17.0