teloclip

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Could you explain in detail how to extend reads?

3

Dear autor： I am assembling a plant genome, and now it is assembled to the level without gap. It have 21 chromosomes, but so far only 39 have been counted,...

zhangwenda0518

Adamtaranto

Confusing about input and output file

17

Dear Adam, It is amazing to find such a great tool for telomere anchoring! But I would like to say some expression you mentioned in the tutorial is blurred, especially...

cyycyj

Feature: Align and Extend

5

Existing modules: - Base Teloclip extracts any reads that are soft-clipped at contig ends (optionally checking for telomeric motifs) - Teloclip-extract: bins reads from teloclip into output files per contig...

Adamtaranto

Add metadata to extracted overhang reads

1

`teloclip-extract` will write reads with terminal clipped-overhangs to fasta files. To aide in sanity checks we should include some metadata to the fasta header. Proposed fields: - Anchor len: how...

Adamtaranto

Motif runs in clipped regions of raw ONT reads may contain homopolymer errors where the number of sequential repeated bases is incorrect. Currently `teloclip` has an option `--noPoly` which compresses...

Adamtaranto

Automatically extend contigs

1

Hi, I am wondering is there any way (not the manual checking) to extend the contigs according to the telomere overhangs identified? Thx

ihbxiongjie

Continuing from issue #13. Update codebase to improve readability. Tasks include: Add typehints Update logging Add Docstrings Split long functions into sub-functions

Adamtaranto

Automate testing

1

- Add test cases for core functions. - Add github action to run test on PRs

Adamtaranto

Package Distribution

1

- Add github action to package and push to pypi on new release - Update Bioconda version

Adamtaranto