Sequencing calculators

Single-purpose tools that compute as you type. Everything runs in your browser — nothing is uploaded.

Sequencing

• Sequencing coverage calculator Work out mean depth of coverage from genome size, read length and read count — or the number of reads you need to hit a target depth.
• Coverage gap estimator Use the Lander–Waterman model to estimate what fraction of a genome is left uncovered at a given mean depth, and how many gaps to expect.
• Variant detection power Compute the probability of seeing at least k alternate reads for a variant at a given allele fraction and depth — or the minimum depth to reach a target power.

Library prep

• ng/µL ⇄ nM converter Convert dsDNA concentration between mass units (ng/µL) and molarity (nM) for a fragment of a given length. Essential for library pooling and loading.
• Library dilution calculator Work out how much stock and diluent to mix to reach a target loading concentration in a target final volume. Stock can be in ng/µL or nM.
• Molarity to copy number Convert a molar concentration (nM) and a sample volume into the number of molecules (copies), using Avogadro’s number.
• Library pooling calculator Pool several libraries to equimolar (or read-share weighted) ratios. Enter each sample’s concentration and fragment length to get the volume of each to add for a target pool volume.
• Oligo resuspension calculator Work out the volume of buffer to add to a dried oligo to reach a target stock concentration, from the amount supplied in nmol.
• Ligation molar ratio Compute the insert mass needed for a target insert:vector molar ratio in a ligation, from vector mass and the two fragment lengths.
• Flow-cell loading converter Convert a loading concentration from one platform to another by proportion. You supply each platform’s recommended optimum — no instrument values are baked in.

PCR & primers

• Primer melting temperature (Wallace rule) Estimate the melting temperature of a short DNA oligo with the Wallace "2 + 4" rule, plus GC content, length and reverse complement.
• Primer-dimer checker Check a primer pair for self- and cross-dimer risk by scanning 3′ ends for complementary runs, and report each primer’s 3′ GC clamp.
• Degenerate primer complexity Count how many distinct sequences a degenerate oligo represents, from its IUPAC ambiguity codes — the product of the possibilities at each position.
• Nearest-neighbour melting temperature A more accurate primer Tm than the Wallace rule, using SantaLucia 1998 nearest-neighbour thermodynamics with salt and primer-concentration corrections.

Sequence utilities

• Reverse complement Get the reverse complement of a DNA sequence (5′ → 3′), with its length and GC content. Accepts A, C, G, T and N.
• GC content calculator Calculate the percentage of G and C bases in a DNA sequence, with base counts. Handy for primer design and assessing sequence composition.
• ORF finder Find open reading frames (ATG to stop) in the three forward frames of a DNA sequence and translate each to protein, with frame, position and length.
• Six-frame ORF finder Find open reading frames in all six reading frames — three forward and three on the reverse-complement strand — and translate each to protein.
• Protein molecular weight Estimate the molecular weight of a protein in Da/kDa from its single-letter amino-acid sequence, using standard average residue masses.
• Restriction enzyme cutter Scan a DNA sequence for cut sites of a curated set of common restriction enzymes (EcoRI, BamHI, HindIII, NotI and more), with position and cut offset.

Quality scores

• Phred quality score converter Convert between a Phred quality score (Q) and base-call accuracy / error probability, both directions. Q30 means 99.9% accuracy.

Quality control

• FASTQ quality check Drop in a .fastq or .fastq.gz file to see read count, read-length distribution, GC content and per-base quality — computed entirely in your browser.
• Sequencing file size estimator Estimate FASTQ (raw + gzip) or BAM file size from read count, read length and layout. BAM is a rough approximation, since real sizes vary with data.
• Sequencing adapter lookup Identify which common sequencing adapter an over-represented sequence matches (Illumina TruSeq, Nextera and more), by exact-substring matching.

Planning

• Sequencing cost calculator Turn your own quoted run price into cost per sample, per Gb and per genome. All prices are your inputs — no vendor pricing is built in or implied.
• RNA-seq read estimator A rough planning estimate of reads needed per sample for RNA-seq, from the number of features and a target average reads per feature. Not a power calculation.