BIONODE Open Access Tools

Function

Replaces original FASTQ read identifiers with new sequential IDs generated from a user-defined prefix while preserving the sequence and quality information.

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Input Format

• FASTQ files (.fastq, .fq)
• Compressed FASTQ files (.fastq.gz, .fq.gz)
• Custom prefix for read names.

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Output Format

• FASTQ file with renamed identifiers.
• Sequence lines remain unchanged.
• Quality scores remain unchanged.
• IDs become sequential: @prefix_1, @prefix_2, etc.

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Applications

• Standardizing read names.
• Sample-specific tagging.
• Data anonymization.
• Preventing duplicate IDs after merging.
• Improving compatibility with downstream tools.

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Example

Original

@NB551234:45:H7F2...
ATCGATCG
+
FFFFFFFF

↓

Prefix = sample_

@sample_1
ATCGATCG
+
FFFFFFFF

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SeqKit Example

seqkit replace \
-p '.+' \
-r 'sample_{nr}' \
input.fastq.gz \
-o renamed.fastq.gz

AWK Example

awk '
BEGIN{i=1}
NR%4==1{
print "@sample_"i
i++
next
}
{print}
' input.fastq \
> renamed.fastq

Compressed FASTQ Example

zcat input.fastq.gz | \
awk '
BEGIN{i=1}
NR%4==1{
print "@sample_"i
i++
next
}
{print}
' | gzip \
> renamed.fastq.gz

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Suggested Reading

• SeqKit Documentation
• BBTools Documentation
• Biopython Documentation

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