BIONODE Open Access Tools

Function

Generates the reverse complement of each read in a FASTQ file. Sequences are reversed and complemented (A↔T, C↔G), while quality score strings are reversed to maintain base-quality correspondence.

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Input Format

• FASTQ files (.fastq, .fq)
• Compressed FASTQ files (.fastq.gz, .fq.gz)
• Optional output file name.

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Output Format

• Reverse-complemented FASTQ file.
• Read identifiers remain unchanged.
• Quality scores are reversed.
• Same number of reads as input.

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Applications

• Strand correction.
• Preparing reads for downstream tools.
• Adapter and primer analysis.
• Handling reverse-strand sequencing protocols.
• Comparative motif analysis.

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Example

Original

@read1
ATCG
+
FFFF

↓

@read1
CGAT
+
FFFF

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SeqKit Example

seqkit seq -r -p \
input.fastq.gz \
-o revcomp.fastq.gz

FASTX Toolkit Example

fastx_reverse_complement \
-i input.fastq \
-o revcomp.fastq

Biopython Example

from Bio import SeqIO

with open("revcomp.fastq", "w") as out:
    for record in SeqIO.parse(
            "input.fastq",
            "fastq"):
        SeqIO.write(
            record.reverse_complement(
                id=record.id,
                description=""
            ),
            out,
            "fastq"
        )

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Suggested Reading

• SeqKit Documentation
• FASTX Toolkit
• Biopython Documentation

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