Comments (1)
There is a secondary tool packaged with teloclip called teloclip-extract
, this tool will output all the overhangs for each end of each contig.
The overhanging region of each read is in lowercase in the output files. You can selected the longest overhang and manually append it to the relevant contig.
Alternatively, you can assemble all the overhanging reads with miniasm which should give a single contig if all reads were correctly mapped and then re-process this new contig with teloclip-extract to get a single overhang segment with which to extend your contig.
Remember to polish your extended contigs with long-read (Racon) and/or short-read (Pilon) polishers.
I might automate the process later but it will always be best to manually inspect the alignments to avoid introducing errors
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Related Issues (20)
- error "invalid mode: 'rU' " in teloclip (v. bioconda)
- Refresh codebase
- Automate testing HOT 1
- Package Distribution HOT 1
- Feature: Align and Extend HOT 5
- No 'rU' option in Python 3.12 HOT 4
- Improve readability
- Confusing about input and output file HOT 17
- Feature: Fuzzy motif search
- Add metadata to extracted overhang reads HOT 1
- Missing isMotifInClip()
- Could you explain in detail how to extend reads? HOT 3
- Calculate alignment end position from CIGAR HOT 1
- Verify: Correct read slice coords for negative strand alignments HOT 2
- Summary report option
- Interactive Contig extension HOT 1
- functionality to extract reads at NNN gaps in scaffolds? HOT 2
- NNNNN reads HOT 8
- Find existing telo repeats in contigs HOT 1
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