bedtools/bedtools_spacing

genomics

intervals

spacing

gaps

distance

distribution

clustering

Description

Calculate gaps between adjacent genomic intervals within each chromosome.

bedtools spacing analyzes sorted genomic intervals and reports the gap length
between each interval and its predecessor on the same chromosome. The gap distances
are added as an additional column to the output, providing insight into the spatial
distribution of features.

This tool is commonly used for:

Analyzing spacing patterns in genomic features
Quality control of interval datasets and their density
Identifying clustering or regular spacing in genomic data
Preprocessing for downstream spatial analysis
Detecting overlapping or adjacent intervals in datasets
Statistical analysis of genomic feature distribution

Type

bash_script

License

MIT

Keywords

genomics

intervals

spacing

gaps

distance

distribution

clustering

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.bed"  
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_spacing/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input file containing genomic intervals for spacing analysis. Format: BED, GFF, VCF, or BAM file Content: Genomic intervals to analyze for gap spacing Requirements: Must be sorted by chromosome and start coordinate (sort -k1,1 -k2,2n) Output: Original intervals with gap distances appended as last column

Name

Type & Properties

--input

-i

file

required

Outputs

Name	Type & Properties	Description
--output	file required output	Output file with gap spacing information appended. Format: Same format as input with additional spacing column Content: Original intervals plus gap distances in the last column Gap values: - "." for first interval on each chromosome - "0" for adjacent intervals - "-1" for overlapping intervals - Positive integers for gap sizes

Name

Type & Properties

--output

file

required

output

Format Options

Name	Type & Properties	Description
--output_bed -bed	boolean_true	Convert BAM input to BED format output. Usage: Only applicable when input is BAM format Effect: Output genomic coordinates in BED format instead of maintaining BAM format Applications: Converting alignment data to interval format with spacing information Default: false (maintain input format)
--include_header -header	boolean_true	Include the original file header in output. Usage: Preserves metadata and format information from input Applications: Maintaining file structure and annotations Formats: Particularly relevant for VCF and GFF files Default: false (no header included)

Name

Type & Properties

--output_bed

-bed

boolean_true

--include_header

-header

boolean_true

Performance Options

Name	Type & Properties	Description
--no_buffer -nobuf	boolean_true	Disable output buffering for real-time processing. Effect: Each line printed immediately instead of buffered Trade-off: Slower output but enables real-time processing Applications: Pipeline integration, streaming analysis Default: false (buffered output for performance)
--input_buffer -iobuf	string	Amount of memory to allocate for input buffer. Format: Integer with optional K/M/G suffix Examples: "1G", "512M", "2048K" Usage: Larger buffers can improve I/O performance for large files Note: Currently has no effect with compressed files

Name

Type & Properties

--no_buffer

-nobuf

boolean_true

--input_buffer

-iobuf

string