BIONODE Open Access Tools

Function

Combines paired-end FASTQ files (R1 and R2) into a single interleaved FASTQ file where each forward read is immediately followed by its corresponding reverse read.

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Input Format

• R1 FASTQ file (.fastq, .fq, .fastq.gz)
• R2 FASTQ file (.fastq, .fq, .fastq.gz)
• Both files must contain the same reads in the same order.

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Output Format

• Single interleaved FASTQ file.
• Reads appear as R1 → R2 → R1 → R2.
• Original FASTQ records are preserved.

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Applications

• BWA MEM paired-end alignment.
• Bowtie2 interleaved input.
• Assembly pipelines.
• Streaming paired-end workflows.
• Simplified file management.

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Example

R1.fastq

Read1/1
Read2/1

+

R2.fastq

Read1/2
Read2/2

↓

Interleaved.fastq

Read1/1
Read1/2
Read2/1
Read2/2

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SeqKit Example

seqkit pair \
-1 R1.fastq.gz \
-2 R2.fastq.gz | \
seqkit interleaved \
-o interleaved.fastq.gz

BBMap Example

reformat.sh \
in1=R1.fastq.gz \
in2=R2.fastq.gz \
out=interleaved.fastq.gz

BWA Example

bwa mem -p \
reference.fa \
interleaved.fastq \
> aligned.sam

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Suggested Reading

• SeqKit Documentation
• BBTools Documentation
• BWA Documentation
• Bowtie2 Documentation

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