blast_blastn

Tags: blast blastn alignment dna search fasta sample-scope

Search a nucleotide database using a nucleotide query.

Uses BLASTN to align nucleotide query sequences (FASTA) against a nucleotide BLAST database. It is optimized for finding highly similar sequences.

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 nucleotide query sequences

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 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

Parameter	Type	Default	Description
`--blastn_query`	string		A fasta file containing the query sequences to BLAST against the database
`--blastn_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
`--blastn_opts`	string		Additional options to pass to BLASTN
`--blastn_perc_identity`	integer	`50`	Percent identity
`--blastn_qcov_hsp_perc`	integer	`50`	Percent query coverage per hsp
`--blastn_max_target_seqs`	integer	`2000`	Maximum number of aligned sequences to keep

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)

BLAST_BLASTN:
    - blast: 2.17.0