BIONODE Open Access Tools

Function

Filters FASTQ or FASTA sequences based on user-defined minimum and maximum length thresholds. Reads outside the specified range are removed from the output.

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Input Format

• FASTQ files (.fastq, .fq)
• FASTA files (.fasta, .fa, .fna)
• Compressed files (.gz)
• User-defined minimum and/or maximum sequence length.

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Output Format

• Filtered FASTQ or FASTA file.
• Output format remains identical to the input format.
• Only sequences within the selected length range are retained.

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Applications

• Remove short low-information reads.
• Eliminate extremely long outlier reads.
• Prepare datasets for assembly.
• Standardize read lengths.
• Select reads matching expected amplicon or feature sizes.

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Example

Input Reads

25 bp
80 bp
150 bp
400 bp

Minimum Length = 50
Maximum Length = 300

↓

Retained Reads

80 bp
150 bp

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SeqKit Example

seqkit seq \
-m 50 \
-M 300 \
input.fastq.gz \
-o filtered.fastq.gz

FASTA Example

seqkit seq \
-m 50 \
-M 300 \
input.fasta \
-o filtered.fasta

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Suggested Reading

• SeqKit Documentation
• NanoFilt
• Biopython Documentation

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