abif-ts

TypeScript parser for Applied Biosystems ABIF (.ab1) Sanger sequencing files.

Extracts called sequence, Phred quality scores, raw fluorescence trace data, peak positions, and run metadata. Works in the browser (ArrayBuffer) and Node.js (Buffer). Zero dependencies.

Installation

npm install @shandley/abif-ts
# or
pnpm add @shandley/abif-ts

Quick start

import { parseAbif } from "@shandley/abif-ts";

// Browser: read a File from <input type="file">
const buffer = await file.arrayBuffer();
const read = parseAbif(buffer);

console.log(read.sequence);       // "ATGCAAGTCCG..."
console.log(read.qualityScores);  // [28, 40, 38, ...]  (Phred scores)
console.log(read.sampleName);     // "sample_F"
console.log(read.traces.A);       // Int16Array of fluorescence values
console.log(read.peakPositions);  // [45, 92, 138, ...]

API

parseAbif(buffer: ArrayBuffer): AbifRead

Parse an ABIF file from an ArrayBuffer. Throws if the file is not valid ABIF.

parseAbifFromBase64(base64: string): AbifRead

Parse an ABIF file encoded as a Base64 string.

AbifRead

| Field | Type | Description | |---|---|---| | sequence | string | Called bases (5′→3′) | | qualityScores | number[] | Phred quality scores per base (0–60) | | peakPositions | number[] | Index into trace arrays for each called base | | traces.A/C/G/T | Int16Array | Processed fluorescence traces per channel | | traceLength | number | Number of data points per trace channel | | channelOrder | string | Channel→base mapping (e.g. "ACGT") | | sampleName | string | Sample name from run setup | | dyeSet | string | Dye set / chemistry name | | instrument | string | Instrument model | | runName | string | Run name | | comment | string | Comment field | | directory | DirectoryEntry[] | All raw directory entries for custom access |

Accessing custom tags

import { parseAbif, getTag } from "@shandley/abif-ts";

const read = parseAbif(buffer);
const entry = getTag(read, "TUBE", 1); // lane/tube label

Format reference

ABIF is Applied Biosystems' binary format for Sanger sequencing chromatograms, documented in Applied Biosystems Genetic Analysis Data File Format (2006).

Key tags extracted:

• PBAS 2 — called bases
• PCON 2 — Phred quality scores
• DATA 9-12 — processed fluorescence channels (A/C/G/T)
• PLOC 2 — peak positions
• FWO_ 1 — channel→base order

License

MIT