seqtk/seqtk_subseq

subseq

FASTA

FASTQ

Description

Extract subsequences from FASTA/Q files. Takes as input a FASTA/Q file and a name.lst (sequence ids file) or a reg.bed (genomic regions file).

Type

bash_script

License

MIT

Keywords

subseq

FASTA

FASTQ

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.0 \  
  -main-script target/nextflow/seqtk/seqtk_subseq/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	The input FASTA/Q file.
--name_list	file required	List of sequence names (name.lst) or genomic regions (reg.bed) to extract.

Name

Type & Properties

--input

file

required

--name_list

file

required

Outputs

Name	Type & Properties	Description
--output -o	file required output	The output FASTA/Q file.

Name

Type & Properties

--output

-o

file

required

output

Options

Name	Type & Properties	Description
--tab -t	boolean_true	TAB delimited output.
--strand_aware -s	boolean_true	Strand aware.
--sequence_line_length -l	integer	Sequence line length of input fasta file. Default: 0.

Name

Type & Properties

--tab

-t

boolean_true

--strand_aware

-s

boolean_true

--sequence_line_length

-l

integer