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https://github.com/arangrhie/T2T-Polish
Evaluation and polishing workflows for T2T genome assemblies
https://github.com/arangrhie/T2T-Polish
Last synced: 3 days ago
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Evaluation and polishing workflows for T2T genome assemblies
- Host: GitHub
- URL: https://github.com/arangrhie/T2T-Polish
- Owner: arangrhie
- License: other
- Created: 2020-06-25T16:10:19.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2024-10-16T18:01:58.000Z (3 months ago)
- Last Synced: 2024-10-18T10:04:49.011Z (3 months ago)
- Language: Shell
- Homepage:
- Size: 2.56 MB
- Stars: 102
- Watchers: 9
- Forks: 8
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome_ai_agents - T2T-Polish - Evaluation and polishing workflows for T2T genome assemblies (Building / Workflows)
- awesome_ai_agents - T2T-Polish - Evaluation and polishing workflows for T2T genome assemblies (Building / Workflows)
README
# T2T-Polish
This repository contains up-to-date evaluation and polishing workflows to adapt on general genome assembly projects, with most of the ideas developed and described in [this paper](https://doi.org/10.1038/s41592-022-01440-3).
For exact command lines and workflows used to generate the T2T-CHM13v1.0 and T2T-CHM13v1.1 assemblies, please refer to the [Methods](https://github.com/marbl/CHM13-issues#methods) section in the [CHM13-Issues](https://github.com/marbl/CHM13-issues) repo. Note that some of the tools have been updated since then, and are tracked on this repo.
## Contents
* [QV estimate with hybrid k-mer db](merqury)
* [Homopolymer and 2-mer microsatellite run length comparison](runlength)
* [K\* metric](kmetric)
* Repeat-aware [Winnowmap2 alignments](winnowmap) and [Marker assisted alignment filtering](marker_assisted)
* [Coverage analysis](coverage)
* [Polish SV and SNV like errors through a case study on Chr. 20](doc/T2T_polishing_case_study.md)
* [Legacy automated polishing with Racon + Merfin](automated_polishing) -- Recommend Patrick Grady's: [latest version of Automated polishing](https://github.com/pgrady1322/T2T-Polish)## Related external links
### Variant call, refinements and formatting (Also see [Error Detection](https://github.com/marbl/CHM13-issues/blob/main/error_detection.md))
* [Call SVs and refine sequences](https://github.com/malonge/CallSV)
* [Merge vcfs from Illumina/HiFi and ONT](https://github.com/kishwarshafin/T2T_polishing_scripts/blob/master/polishing_merge_script/vcf_merge_t2t.py)
* [Generate telomere edits](https://github.com/kishwarshafin/T2T_polishing_scripts/blob/master/telomere_variants/generate_telomere_edits.py)### Repeat-aware alignments
* [Winnowmap](https://github.com/marbl/Winnowmap)
* [TandemMapper2 (re-named as VerityMap)](https://github.com/ablab/VerityMap)### Automated polishing
* [Racon](https://github.com/isovic/racon/tree/liftover): Liftover branch for outputting edits in `.vcf`
* [Merfin](https://github.com/arangrhie/merfin): Latest stable code-base### Base level QV estimation
* [Meryl](https://github.com/marbl/meryl)
* [Merqury](https://github.com/marbl/merqury)## Citation
Please cite if any of the codes shared in this repo was used:Mc Cartney AM, Shafin K, Alonge M et al. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. Nat Methods (2022) doi: https://doi.org/10.1038/s41592-022-01440-3