Raw Sanger sequence alignment and merging. Auto gap and mismatch corrections based on AB1 chromatogram file confidence scores. Features batch and single alignment, as well as batch or single merge. Bioinformatics tool for rapid Sanger analysis---automatic alternative to Aliview---AlanView :)
-
Single or batch mode for alignment and merging
-
Auto reverse complementing of reverse reads
Local alignment using Biopython
Auto-correction of:
- Mismatches
- Gaps (based on chromatogram confidence)
- AB1 confidence score-based corrections using customizable thresholds
Input must include:
Two trimmed FASTA files (forward and reverse)
Their corresponding AB1 files
Modes:
Single: Manually select files one by one
Batch: Provide two folders (FASTA and AB1), files are assumed to be ordered as:
| Folder 1 (FASTA) | Folder 2 (AB1) |
|---|---|
| Sample_1.FWD.fas | Sample_1.FWD.ab1 |
| Sample_1.REV.fas | Sample_1.REV.ab1 |
| Sample_2.FWD.fas | Sample_2.FWD.ab1 |
| Sample_2.REV.fas | Sample_2.REV.ab1 |
| ... | ... |
use the sample folders to try for yourself
Reverse complements the reverse primer read
Performs local alignment using pairwise2
Identifies:
Mismatches
Gaps
Calculates the start index of the FASTA read within AB1 using the first 20 bp for mapping
Scores each base with Phred quality scores from AB1:
Uses higher-scoring base to correct mismatch
Deletes gaps from low-quality reads
Skips unresolved regions or flags for manual checking
aligned_files/: Corrected and aligned FASTA files
merged/: Merged consensus sequences
manual_check_required/: Problematic sequences needing manual inspection
Example Output FASTA (from aligned_files/)
HB20_COX-LCO1490 GGTGACCAAAAAATCAAAATAAATGTTGATATAAAATTGGATCTCCACCTCCTATTGGATCAAAAAATGAAGTATT... HB20_COX-HCO2198 ------------------------------------------CTCCACCTCCTATTGGATCAAAAAATGAAGTATT...
Trim poor-quality AB1 reads before running
Confidence threshold in corrections is customizable (confidence_threshold=20 by default)
Alignment and merging are decoupled for flexibility
Python 3.7+ Dependencies (included in requirements.txt): biopython tkinter (preinstalled with most Python versions)