Split FASTA / FASTQ Files

Split large FASTA or FASTQ files into smaller chunks

Multiple files allowed | Maximum size: 500 MB per file
For FASTQ files, use multiples of 4 to preserve read structure.

Split FASTA / FASTQ Files

Function

Splitting FASTA or FASTQ files is a common bioinformatics operation where large sequence files are divided into smaller chunks based on a specified number of lines. This simplifies data management and enables parallel processing workflows.

Input Format

  • FASTA files (.fasta, .fa, .fna)
  • FASTQ files (.fastq, .fq)
  • Compressed FASTA/FASTQ files (.gz)
  • Number of lines per output file

Output Format

  • Multiple smaller FASTA or FASTQ files.
  • Output format remains identical to input format.
  • Each chunk contains the specified number of lines.

Applications

  • Parallel processing on HPC clusters.
  • Breaking large datasets into manageable chunks.
  • Pipeline distribution and workflow optimization.
  • Testing and debugging bioinformatics pipelines.
  • Efficient storage and transfer of sequencing data.

Example Usage

Split a FASTQ file into chunks of 40,000 lines: 

split -l 40000 input.fastq chunk_

Split a FASTA file by sequence count using SeqKit: 

seqkit split2 -s 10000 input.fasta -O split_output/

Suggested Reading

Important Notes:
  • FASTQ files contain 4 lines per read.
  • Always use multiples of 4 when splitting FASTQ files.
  • Very large files may take additional processing time.
  • Sequence-aware tools such as SeqKit are preferred for FASTA sequence-based splitting.
  • Multiple input files can be uploaded and processed together.