BIONODE Open Access Tools

Function

Randomly selects a fraction of reads from a FASTQ file to generate a smaller but representative dataset. An optional random seed allows reproducible sampling.

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Input Format

• FASTQ files (.fastq, .fq)
• Compressed FASTQ files (.fastq.gz, .fq.gz)
• Sampling fraction between 0 and 1
• Optional random seed

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Output Format

• FASTQ file containing a randomly selected subset of reads.
• Original read structure and quality scores are preserved.

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Applications

• Pipeline testing.
• Reducing computational requirements.
• Benchmarking workflows.
• Quality-control spot checks.
• Normalizing sequencing depth between samples.

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SeqKit Example

seqkit sample \
-p 0.1 \
-s 42 \
input.fastq.gz \
-o subsampled.fastq.gz

SeqTK Example

seqtk sample \
-s 42 \
input.fastq.gz \
0.1 > subsampled.fastq

Paired-End Example

seqtk sample -s 42 R1.fastq.gz 0.1 \
> R1_sub.fastq

seqtk sample -s 42 R2.fastq.gz 0.1 \
> R2_sub.fastq

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Suggested Reading

• SeqKit Documentation
• SeqTK Documentation
• BBTools Documentation
• Biopython Documentation

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