FASTA splitter

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Split FASTA files into smaller files by number of sequences or target number of outputs.

Input
FASTA only. This tool returns a ZIP archive containing split FASTA files and a report.
Plain-text FASTA recommended. Processed synchronously.
Split mode
Each output file will contain up to this many FASTA records.
Records will be distributed as evenly as possible across this many files.
Sequence-ID naming is available only when each output file contains exactly one record.
Limits: up to 15 MB (uncompressed) • up to 400,000 records

About this tool

FASTA Splitter splits FASTA files into multiple smaller files by number of records per file or by target number of output files. Output is deterministic and returned as a ZIP archive with a report. If the requested split would create more than the allowed number of output files, the tool returns an error. For inspecting dataset size and distribution before splitting, use Sequence stats. For FASTA structure details, see FASTA format reference.

For larger datasets, multi-file runs, or more involved workflows, this can be executed separately as a custom analysis.

Tool guarantees
  • ✓ No hidden transformations
  • ✓ Input processed only for this request
  • ✓ FASTA structure preserved in output

Results

Submit input to see results here.
Running analyses at scale?
We execute bioinformatics analyses and data-processing workflows on your data.
Useful for larger datasets, multiple files, or tasks that are not convenient to run locally.
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  • Split by records per file: output files are created in input order, and the last file may contain the remainder.
  • Split into N files: records are distributed as evenly as possible.
  • Output file limit: if the requested split would create too many output files, the tool returns an error rather than silently changing the split behavior.
  • Archive format: the download is a ZIP archive containing plain FASTA files and a report.