BIONODE Open Access Tools

Function

Count Reads reports the total number of reads (FASTQ) or sequences (FASTA) in one or more input files. Optional statistics include total bases, average read length, and read-length distributions.

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Input Format

• FASTQ files (.fastq, .fq)
• FASTA files (.fasta, .fa, .fna)
• Compressed files (.gz)
• Multiple files can be analyzed together.

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Output Format

• Read or sequence count.
• Total base count.
• Average read length.
• Read length histogram (optional).
• Text, TSV or JSON output.

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Applications

• Sequencing QC.
• Sample size verification.
• Dataset size estimation.
• Pipeline validation.
• Read length assessment.

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Example Usage

Count reads in FASTQ:

echo $(wc -l < sample.fastq) / 4 | bc

Count reads in compressed FASTQ:

echo $(zcat sample.fastq.gz | wc -l) / 4 | bc

Count sequences in FASTA:

grep -c "^>" sample.fasta

Using SeqKit:

seqkit stats sample.fastq.gz

seqkit stats *.fastq.gz

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Suggested Reading

• SeqKit Documentation
• FASTX Toolkit
• BBTools
• Samtools

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