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).
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. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o | file required output | The output FASTA/Q file. |
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. |
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 v0.2.0 \
-main-script target/nextflow/seqtk/seqtk_subseq/main.nf \
-params-file params.yaml Relationships
Used by
0 relationships
No components use this component.
Current component
seqtk/seqtk_subseqbiobox v0.2.0
Uses
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No component dependencies found.