https://github.com/sam-k/seq-quality-trimming
Trimming Sanger sequencing reads by quality
https://github.com/sam-k/seq-quality-trimming
dna genomics metabarcoding sequencing ta-cloning
Last synced: 6 months ago
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Trimming Sanger sequencing reads by quality
- Host: GitHub
- URL: https://github.com/sam-k/seq-quality-trimming
- Owner: sam-k
- Created: 2019-01-17T21:42:28.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2019-03-07T01:57:16.000Z (over 6 years ago)
- Last Synced: 2025-04-19T23:54:15.954Z (6 months ago)
- Topics: dna, genomics, metabarcoding, sequencing, ta-cloning
- Language: Python
- Homepage:
- Size: 16.6 KB
- Stars: 6
- Watchers: 0
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# seq-quality-trimming
Trimming and merging reads from .ab1 Sanger sequencing files.
Part of the [human diet quantification project](http://el.ladlab.org:8080/), which aims to establish a model for quantifying dietary components from DNA metabarcoding data.
## Quality trimming
- Isolate segment with the highest quality from the sequence, using Kadane's algorithm.
- Trim low-quality ends of the sequence.
## Merging reads
- Align the forward/reverse PCR products using the Smith-Waterman algorithm for local alignment.
- Merge the reads if the overlap is large enough.
## BLAST
- BLAST the merged sequence.