ab1lens

ab1lens visualizes Sanger sequencing chromatograms in AB1/ABIF and SCF format, and .srd raw files from the Nanofor-05 capillary sequencer, enabling local inspection of traces, base calls, quality values, and reference alignments entirely within the browser.

Key Features:

• Chromatogram Viewing: Displays raw and analysed traces, base calls (called or edited), and per-base quality values.
• ABIF Directory Inspection: Shows the full ABIF directory contents for comprehensive file metadata access.
• Dual Read Comparison: Places two reads side by side with their tag tables aligned for comparative analysis.
• Reference Alignment: Aligns a read against a pasted or loaded reference, reporting identity, mismatches, indels, and unaligned ends, with automatic strand flipping when the read maps to the opposite strand.
• End Trimming: Implements modified Mott or sliding window trimming with draggable handles for interactive adjustment.
• IUPAC-Aware Motif Search: Searches for motifs including primers with IUPAC nucleotide code support.
• QC Metrics Export: Copies quality control metrics as CSV for downstream analysis.
• Region Selection and Export: Allows drag-selection of a base range for copying as FASTA, zooming, or exporting that specific region.
• File Export: Exports reads as FASTA, FASTQ, .qual, or ABIF, and chromatograms as high-resolution PNG.
• Local Session Storage: Maintains open files as local sessions without server upload.

Scientific Applications:

• Sanger Sequencing Quality Control: Inspects raw and analysed chromatogram traces, base calls, and per-base quality values to assess sequencing run quality.
• Sequence Verification: Aligns reads against reference sequences to identify mismatches, indels, and unaligned regions for confirming expected sequences.
• Primer and Motif Analysis: Searches for primers and other sequence motifs using IUPAC-aware pattern matching in chromatogram data.
• Data Conversion and Export: Converts sequencing reads between formats (FASTA, FASTQ, ABIF) and generates publication-quality chromatogram images.
• Privacy-Sensitive Sequence Analysis: Processes unpublished and clinical sequencing data locally without server upload for compliance with data protection requirements.

Methodology:

ab1lens runs entirely in the browser with files opened locally and never uploaded to a server; .srd raw files from the Nanofor-05 capillary sequencer are converted to ABIF upon opening; end trimming uses modified Mott or sliding window algorithms; reference alignment reports identity, mismatches, indels, and unaligned ends with automatic strand flipping.