Thanks to visit codestin.com
Credit goes to github.com

Skip to content

Citation for damageprofiler #730

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
apeltzer merged 3 commits into from
Apr 26, 2021
Merged

Citation for damageprofiler #730

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
aa4d0a6
Citation for damageprofiler
apeltzer Apr 25, 2021
e84cf29
Update CHANGELOG.md
jfy133 Apr 25, 2021
380374c
Merge branch 'dev' into dmgprof-add-citation
jfy133 Apr 25, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

- Corrected explanation of the "--min_adap_overlap" parameter for AdapterRemoval in the docs
- [#725](https://github.com/nf-core/eager/pull/725) `bwa_index` doc update
- Updated DamageProfiler citation from bioRxiv to publication

### `Dependencies`

Expand Down
2 changes: 1 addition & 1 deletion README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -207,7 +207,7 @@ In addition, references of tools and data used in this pipeline are as follows:
* **AdapterRemoval v2** Schubert, M., Lindgreen, S., & Orlando, L. (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 9, 88. [https://doi.org/10.1186/s13104-016-1900-2](https://doi.org/10.1186/s13104-016-1900-2). Download: [https://github.com/MikkelSchubert/adapterremoval](https://github.com/MikkelSchubert/adapterremoval)
* **bwa** Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics , 25(14), 1754–1760. [https://doi.org/10.1093/bioinformatics/btp324](https://doi.org/10.1093/bioinformatics/btp324). Download: [http://bio-bwa.sourceforge.net/bwa.shtml](http://bio-bwa.sourceforge.net/bwa.shtml)
* **SAMtools** Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., … 1000 Genome Project Data Processing Subgroup. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics , 25(16), 2078–2079. [https://doi.org/10.1093/bioinformatics/btp352](https://doi.org/10.1093/bioinformatics/btp352). Download: [http://www.htslib.org/](http://www.htslib.org/)
* **DamageProfiler** Neukamm, J., Peltzer, A., & Nieselt, K. (2020). DamageProfiler: Fast damage pattern calculation for ancient DNA. In biorXiv (p. 2020.10.01.322206). [https://doi.org/10.1101/2020.10.01.322206](https://doi.org/10.1101/2020.10.01.322206). Download: [https://github.com/Integrative-Transcriptomics/DamageProfiler](https://github.com/Integrative-Transcriptomics/DamageProfiler)
* **DamageProfiler** Neukamm, J., Peltzer, A., & Nieselt, K. (2020). DamageProfiler: Fast damage pattern calculation for ancient DNA. In Bioinformatics (btab190). [https://doi.org/10.1093/bioinformatics/btab190](https://doi.org/10.1093/bioinformatics/btab190). Download: [https://github.com/Integrative-Transcriptomics/DamageProfiler](https://github.com/Integrative-Transcriptomics/DamageProfiler)
* **QualiMap** Okonechnikov, K., Conesa, A., & García-Alcalde, F. (2016). Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics , 32(2), 292–294. [https://doi.org/10.1093/bioinformatics/btv566](https://doi.org/10.1093/bioinformatics/btv566). Download: [http://qualimap.bioinfo.cipf.es/](http://qualimap.bioinfo.cipf.es/)
* **preseq** Daley, T., & Smith, A. D. (2013). Predicting the molecular complexity of sequencing libraries. Nature Methods, 10(4), 325–327. [https://doi.org/10.1038/nmeth.2375](https://doi.org/10.1038/nmeth.2375). Download: [http://smithlabresearch.org/software/preseq/](http://smithlabresearch.org/software/preseq/)
* **PMDTools** Skoglund, P., Northoff, B. H., Shunkov, M. V., Derevianko, A. P., Pääbo, S., Krause, J., & Jakobsson, M. (2014). Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal. Proceedings of the National Academy of Sciences of the United States of America, 111(6), 2229–2234. [https://doi.org/10.1073/pnas.1318934111](https://doi.org/10.1073/pnas.1318934111). Download: [https://github.com/pontussk/PMDtools](https://github.com/pontussk/PMDtools)
Expand Down