FASTA length filter

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Filter FASTA sequences by length using minimum and maximum thresholds. Keep or remove records and generate a clean FASTA output for downstream analysis.

Input
FASTA only. Thresholds apply to sequence length after sequence lines are joined within each record.
Plain-text FASTA recommended. Processed synchronously.
Action
Keep/remove records with length ≥ this value.
Keep/remove records with length ≤ this value.
Limits: up to 15 MB (uncompressed) • up to 500,000 records

About this tool

FASTA Length Filter filters FASTA records by sequence length using minimum and/or maximum thresholds. You can keep or remove matching records and return a clean, deterministic FASTA output. Sequence length filters are inclusive: minimum means length ≥ minimum, and maximum means length ≤ maximum. This is commonly used to remove short contigs, retain amplicons within expected size ranges, or prepare subsets before downstream analysis. For summary statistics (N50, length distribution, GC%), use Sequence stats. For definitions of length metrics, see sequence statistics reference.

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

Results

Submit input to see results here.

  • Sequence length: number of sequence characters after FASTA sequence lines are joined within a record.
  • Keep matching records: retain records whose lengths are within the requested range.
  • Remove matching records: discard records whose lengths are within the requested range and keep the rest.
  • Thresholds: you may provide only a minimum length, only a maximum length, or both.
  • Determinism: headers are preserved and records are not reordered.

  • Remove very short contigs, probes, or low-information fragments.
  • Keep records within an expected amplicon or barcode length range.
  • Create a quick deterministic subset before downstream analysis.
  • Inspect the effect of simple size thresholds without installing local tools.