Bench Tools Free browser-based calculators for the lab and for bioinformatics

Tools›Sequence tools

FASTA File Statistics: Sequence Count, Length Distribution, and N50

Paste a multi-FASTA file and instantly get sequence count, total length, N50/L50, GC%, and length distribution.

The first thing to do with a new assembly or a batch of sequences is examine the summary statistics.

N50 is the most commonly misunderstood metric. The definition: sort all contigs by length from longest to shortest, then accumulate lengths until the running total first reaches half the total assembly length — the length of the contig at that point is the N50. It measures “assembly contiguity” — a larger N50 means longer fragments account for a greater share of the assembly.

L50 is the number of contigs needed to reach half the total length. N50 and L50 are a pair, and they move in opposite directions.

One well-known caveat: N50 is sensitive to total assembly length. If many short contigs are missing from the assembly, the total length shrinks and the N50 can look artificially inflated. N50 must always be read alongside total length and sequence count; the number alone is meaningless.

All calculations are performed in the browser — sequences are never uploaded. For large files, working with a subset first is advisable.

FAQ

Is a larger N50 always better?

Only when total length and completeness are comparable. N50 is sensitive to total assembly length — dropping large numbers of short contigs inflates N50 artificially, so it must be interpreted together with total length, sequence count, and BUSCO completeness.

How large a file can it handle?

Browser memory is the limiting factor. Files of several tens of megabytes are generally fine; for a full mammalian genome, processing locally with a command-line tool is recommended.

Related tools

Protein Molecular Weight, Isoelectric Point & 280 nm Extinction Coefficient Calculator

Enter an amino acid sequence to compute molecular weight, theoretical pI, molar extinction coefficient, and A280 at 1 mg/mL.

Pairwise Sequence Alignment Online Tool (Needleman-Wunsch Global Alignment)

Global alignment of two sequences with alignment output, score, percent identity, and mismatch/gap statistics.

Codon Table Quick Reference (Standard Genetic Code): Bidirectional Codon–Amino Acid Lookup

All 64 codons of the standard genetic code — look up amino acids by codon or reverse-query codons by amino acid; accepts both DNA and RNA notation.
No ads, no tracking, no sign-up — and every formula here is checked against a known answer. Keeping it that way takes ongoing work. If it saved you time, buy me a coffee.
Buy me a coffee