Genome Sequencing & Assembly Simulator

Shotgun Sequencing

Read length 180 bp

Coverage 4.0×

Sequencing error rate 1.0%

Min overlap to merge 24 bp

Contigs

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Largest contig

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Genome covered

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Mean depth

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How it works

Shotgun sequencing breaks many copies of a genome into short overlapping fragments (reads) whose exact starting position is unknown. Assembly reconstructs the genome by finding reads whose ends overlap — where the tail of one read matches the head of another for at least a minimum length — and greedily stitching them into longer contiguous sequences ("contigs"). Sequencing errors corrupt individual bases, which can shrink or destroy a true overlap and fragment the assembly.

reads ≈ coverage · genomeLen / readLen
P(gap at a base) ≈ e^(−coverage)     (Lander–Waterman)
merge(A,B) if overlap(A,B) ≥ minOverlap · (1 − errorRate)^k

Read length — longer reads carry more overlap signal per fragment and survive more sequencing errors intact.
Coverage — average number of reads covering each base; low coverage leaves gaps nothing sequenced at all.
Sequencing error rate — per-base miscall probability; it silently shortens the overlap two reads can actually agree on.
Min overlap to merge — how much matching sequence the assembler demands before joining two reads; too low risks false joins, too high fragments the assembly unnecessarily.

Real-world relevance: this overlap–layout–consensus loop is the classical approach behind long-read assemblers (used for Sanger and PacBio/Nanopore data); short, error-prone or low-coverage reads are exactly why real genome assemblies come out in many contigs instead of one finished chromosome.

Contig Raw read Error site Gap (uncovered)