bedtools/bedtools_maskfasta

genomics

fasta

masking

sequences

bed

Description

Mask regions in a FASTA file based on genomic coordinates.

bedtools maskfasta masks sequences in a FASTA file based on coordinates defined
in a BED/GFF/VCF file. Masked regions can be replaced with Ns (hard masking),
converted to lowercase (soft masking), or replaced with custom characters.

This tool is commonly used for:

Masking repetitive elements or low-quality regions
Creating masked reference genomes for alignment
Removing specific genomic features from sequences
Preparing sequences for downstream analysis

Type

bash_script

License

MIT

Keywords

genomics

fasta

masking

sequences

bed

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

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

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

Inputs

Name	Type & Properties	Description
--input_fasta -fi	file required	Input FASTA file to mask. Format: FASTA format with nucleotide sequences Content: Reference sequences or assembled contigs Usage: Sequences will be masked at coordinates specified in the BED file Requirements: Must contain sequences referenced in the BED file
--input_bed -bed	file required	BED/GFF/VCF file specifying regions to mask. Format: BED, GFF, or VCF file with genomic coordinates Content: Coordinates of regions to mask in the FASTA file Usage: Each interval defines a region to be masked Requirements: Chromosome names must match FASTA headers

Name

Type & Properties

--input_fasta

-fi

file

required

--input_bed

-bed

file

required

Outputs

Name	Type & Properties	Description
--output -fo	file required output	Output FASTA file with masked sequences. Format: FASTA format with masked sequences Content: Same sequences as input with specified regions masked Masking: Regions replaced with Ns, lowercase, or custom characters

Name

Type & Properties

--output

-fo

file

required

output

Masking Options

Name	Type & Properties	Description
--soft_mask -soft	boolean_true	Use soft masking (lowercase bases) instead of hard masking (Ns). Default: Hard masking with N characters Soft masking: Converts masked regions to lowercase letters Usage: Preserves sequence information while indicating masked regions Applications: Useful for some alignment tools that recognize soft masking
--mask_character -mc	string	Custom character to use for masking instead of N. Default: N (hard masking) or lowercase (soft masking) Usage: Replace masked regions with specified character Example: X, -, or any single character Note: Overrides soft masking when specified
--full_header -fullHeader	boolean_true	Use complete FASTA headers in output. Default: Use only text before first space/tab in header Full header: Preserves entire header line including descriptions Usage: Maintains complete sequence annotations and metadata Applications: Important when headers contain essential information

Name

Type & Properties

--soft_mask

-soft

boolean_true

--mask_character

-mc

string

--full_header

-fullHeader

boolean_true