abif
ABIF (Applied Biosystems Information Format) parser for DNA sequencing data
Summary
| Latest Version | 0.2.0 |
|---|---|
| License | MIT |
| CI Status | Failing |
| Downloads | 0 |
| Last Indexed | 2026-08-27 06:49 |
Tags
Authors
- Andrea Telatin, Claude AI
Installation
nimble install abif
choosenim install abif
git clone https://github.com/quadram-institute-bioscience/nim-abif
OS Compatibility
| Platform | Linux | macOS | Windows | FreeBSD | OpenBSD | NetBSD | Android | iOS | WASM | Embedded |
|---|---|---|---|---|---|---|---|---|---|---|
| abif | ✓ | ✓ | ✓ | - | - | - | - | - | - | - |
Dependencies
| Package | Version | Optional |
|---|---|---|
| nim >= 1.6.0", "nimsvg >= | 0.1.0 | No |
Source
| Repository | https://github.com/quadram-institute-bioscience/nim-abif |
|---|---|
| Homepage | https://quadram-institute-bioscience.github.io/nim-abif |
| Documentation | View Documentation |
| Registry Source | nimble_official |
README
ABIF Parser for Nim
A Nim library to parse ABIF (Applied Biosystems Information Format) files from DNA sequencing machines, commonly used in Sanger capillary sequencing.
Installation
To install the CLI packages:
conda install -c bioconda nim-abif
If you have Nim installed, you can install binaries and library with:
nimble install abif
Usage
Basic Usage
import abif
# Parse a trace file
let trace = newABIFTrace("path/to/trace.ab1")
# Get sequence and quality information
let sequence = trace.getSequence()
let qualityValues = trace.getQualityValues()
let sampleName = trace.getSampleName()
# Export sequence to FASTA format
trace.exportFasta("output.fa")
# Export sequence to FASTQ format
trace.exportFastq("output.fq")
# Don't forget to close the trace when done
trace.close()
Accessing Raw Data
# Get all tag names in the file
let tagNames = trace.getTagNames()
# Access data for a specific tag
let data = trace.getData("PBAS2") # Base calls
let rawData = trace.getData("DATA1") # Raw channel data
Command-line Usage
The library provides three command-line tools:
FASTQ converter with quality trimming
abi2fq trace.ab1 output.fq
The abi2fq tool provides quality-based sequence trimming:
abi2fq --help # Show help message
abi2fq --window=15 --quality=25 trace.ab1 # Trim with window size 15, quality threshold 25
abi2fq --no-trim trace.ab1 # Skip quality trimming
abi2fq --verbose trace.ab1 # Show additional information
abi2fq trace.ab1 # Output to STDOUT
Merging paired (forward/reverse) traces
abimerge forward.ab1 reverse.ab1 merged.fq
The abimerge tool combines forward and reverse Sanger reads using Smith-Waterman alignment:
abimerge --help # Show help message
abimerge --min-overlap=30 fwd.ab1 rev.ab1 # Require at least 30bp overlap
abimerge --score-match=10 --score-mismatch=-8 --score-gap=-10 fwd.ab1 rev.ab1 # Custom alignment scores
abimerge --join=10 fwd.ab1 rev.ab1 # Join seqs with 10 Ns if no overlap found
abimerge --pct-id=90 fwd.ab1 rev.ab1 # Require 90% identity in overlap region
abimerge --verbose fwd.ab1 rev.ab1 # Show alignment details
Render traces
Convert a trace (or part of it) into SVG
abichromatogram tests/A_forward.ab1 -o A.svg -s 500 -e 1000 --width 1600
Data Types
The ABIF format supports various data types, all of which are properly handled by this parser:
- Numeric types (byte, word, short, long, float, double)
- String types (char, pString, cString)
- Date and time values
- Boolean values
Development
Running Tests
nimble test
Building Documentation
nimble docs
License
This library is licensed under the MIT License - see the LICENSE file for details.
Acknowledgments
This Nim implementation is based on: - Co-authored with Claude code - Inspired by Python implementation: abifpy and a Perl implementation: Bio::Trace::ABIF from CPAN