bedtools/bedtools_bamtofastq

Conversion

BAM

FASTQ

Description

Convert BAM alignments to FASTQ files.

This tool extracts FASTQ records from sequence alignments in BAM format,
supporting both single-end and paired-end data extraction.

Type

bash_script

License

MIT

Keywords

Conversion

BAM

FASTQ

Links

Repository

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
fastq: "$id.$key.fastq.fastq"  
fastq2: "$id.$key.fastq2.fastq"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.1 \  
  -main-script target/nextflow/bedtools/bedtools_bamtofastq/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input -i	file required	Input BAM file to be converted to FASTQ. Requirements: - Must be in BAM format - For paired-end output, should be sorted by query name

Name

Type & Properties

--input

-i

file

required

Outputs

Name	Type & Properties	Description
--fastq -fq	file required output	Output FASTQ file for single-end data or first mate in paired-end data. Output format: Standard FASTQ format with sequence and quality scores
--fastq2 -fq2	file output	Output FASTQ file for second mate in paired-end data. Usage: - Required only for paired-end BAM files - BAM should be sorted by query name for proper pairing - If omitted, only first mates or single-end reads are extracted

Name

Type & Properties

--fastq

-fq

file

required

output

--fastq2

-fq2

file

output

Options

Name	Type & Properties	Description
--tags	boolean_true	Create FASTQ based on mate information in BAM R2 and Q2 tags. Usage: - Uses R2 tag for second mate sequence - Uses Q2 tag for second mate quality scores - Alternative to requiring coordinate-sorted paired BAM

Name

Type & Properties

--tags

boolean_true