Concatenate FASTQ Files

Merge two FASTQ or FASTA files into a single output file

Supported formats: FASTQ, FQ, FASTA, FA, FNA and GZIP compressed files (Maximum size: 500 MB per file)

Concatenate FASTQ Files

Function

Concatenation combines multiple sequencing files into a single output file by appending the contents of one file after another. This is a common step in next-generation sequencing (NGS) workflows when sequencing data is distributed across multiple lanes or runs.

Input Format

  • FASTQ files (.fastq, .fq)
  • FASTA files (.fasta, .fa, .fna)
  • Compressed files (.gz)

Output Format

  • Single merged FASTQ file.
  • Single merged FASTA file.
  • Output format automatically follows the uploaded file format.

Applications

  • Merging sequencing lanes.
  • Combining technical replicates.
  • Preparing datasets for alignment.
  • Workflow simplification.
  • Consolidating split sequencing runs.

Example

file1.fastq
    +
file2.fastq

    ↓

concatenated_output.fastq

Linux Example

cat file1.fastq file2.fastq \
> merged.fastq

Compressed Files

cat file1.fastq.gz \
    file2.fastq.gz \
> merged.fastq.gz

Suggested Reading

Important Notes:
  • Upload exactly two files.
  • Files should be of the same format (FASTQ with FASTQ or FASTA with FASTA).
  • Paired-end reads should be concatenated separately for R1 and R2 files.
  • The merged file preserves the original read order.