BIONODE Open Access Tools

Function

Unique Count identifies and counts distinct nucleotide sequences present in FASTQ files. It helps estimate sequence diversity and detect redundancy within sequencing datasets.

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Input Format

• FASTQ files (.fastq)
• Compressed FASTQ files (.fastq.gz)
• Multiple files may be uploaded simultaneously.

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Output Format

• Total number of unique sequences.
• Summary of sequence diversity.

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Applications

• Library complexity assessment.
• Duplicate read detection.
• Sequencing quality control.
• Non-redundant dataset generation.
• Sample comparison across sequencing runs.

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Example Usage

Count unique sequences in a FASTQ file:

awk 'NR%4==2' input.fastq | sort -u | wc -l

For compressed FASTQ files:

zcat input.fastq.gz | awk 'NR%4==2' | sort -u | wc -l

Using SeqKit:

seqkit stats input.fastq.gz

seqkit rmdup -s input.fastq.gz \
-o unique.fastq.gz

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Suggested Reading

• FASTX Toolkit
• SeqKit Documentation
• Biopython Documentation

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