`extract`

It extracts reads classified under a specific taxon. It requires the original FASTA/Q input files and the JOB_ID_classifications.tsv file produced by classify.

Usage

metabuli extract <i:FASTA/Q> <i:classifications> <i:DBDIR> --tax-id TAX_ID [options]

Argument	Description
`FASTA/Q`	The FASTA/Q file(s) used during the `classify` step. Provide two files for paired-end reads.
`classifications`	The `JOB_ID_classifications.tsv` file generated by the `classify` step
`DBDIR`	The same database directory used in the `classify` step
`--tax-id`	Taxonomy ID of the taxon at any rank (e.g., species, genus) from which to extract reads

Examples

Paired-endSingle-endLong-read

metabuli extract read_1.fna read_2.fna JOB_ID_classifications.tsv DBDIR --tax-id TAX_ID

metabuli extract --seq-mode 1 read.fna JOB_ID_classifications.tsv DBDIR --tax-id TAX_ID

metabuli extract --seq-mode 3 read.fna JOB_ID_classifications.tsv DBDIR --tax-id TAX_ID

Output Files

Read type	Output files
Paired-end	`read_1_TAX_ID.fna` and `read_2_TAX_ID.fna`
Single-end or long-read	`read_TAX_ID.fna`