Skip to content
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

Fixed program reference markdown screw up - bold not italics... #93

Merged
merged 1 commit into from
Nov 20, 2018
Merged

Fixed program reference markdown screw up - bold not italics... #93

Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
24 changes: 12 additions & 12 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -86,15 +86,15 @@ do so and everyone is welcome to contribute here!

## Tool References

* *EAGER v1, CircularMapper, DeDup* Peltzer, A., Jäger, G., Herbig, A., Seitz, A., Kniep, C., Krause, J., & Nieselt, K. (2016). EAGER: efficient ancient genome reconstruction. Genome Biology, 17(1), 1–14. [https://doi.org/10.1186/s13059-016-0918-z](https://doi.org/10.1186/s13059-016-0918-z) Download: [https://github.com/apeltzer/EAGER-GUI](https://github.com/apeltzer/EAGER-GUI) and [https://github.com/apeltzer/EAGER-CLI](https://github.com/apeltzer/EAGER-CLI)
* *FastQC* download: [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
* *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* Judith Neukamm (Unpublished)
* *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)
* *MultiQC* Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. [https://doi.org/10.1093/bioinformatics/btw354](https://doi.org/10.1093/bioinformatics/btw354) Download: [https://multiqc.info/](https://multiqc.info/)
* *BamUtils* Jun, G., Wing, M. K., Abecasis, G. R., & Kang, H. M. (2015). An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data. Genome Research, 25(6), 918–925. [https://doi.org/10.1101/gr.176552.114](https://doi.org/10.1101/gr.176552.114) Download: [https://genome.sph.umich.edu/wiki/BamUtil](https://genome.sph.umich.edu/wiki/BamUtil)
* *FastP* Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics , 34(17), i884–i890. [https://doi.org/10.1093/bioinformatics/bty560](https://doi.org/10.1093/bioinformatics/bty560) Download: [https://github.com/OpenGene/fastp](https://github.com/OpenGene/fastp)
* **EAGER v1**, CircularMapper, DeDup* Peltzer, A., Jäger, G., Herbig, A., Seitz, A., Kniep, C., Krause, J., & Nieselt, K. (2016). EAGER: efficient ancient genome reconstruction. Genome Biology, 17(1), 1–14. [https://doi.org/10.1186/s13059-016-0918-z](https://doi.org/10.1186/s13059-016-0918-z) Download: [https://github.com/apeltzer/EAGER-GUI](https://github.com/apeltzer/EAGER-GUI) and [https://github.com/apeltzer/EAGER-CLI](https://github.com/apeltzer/EAGER-CLI)
* **FastQC** download: [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
* **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** Judith Neukamm (Unpublished)
* **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)
* **MultiQC** Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. [https://doi.org/10.1093/bioinformatics/btw354](https://doi.org/10.1093/bioinformatics/btw354) Download: [https://multiqc.info/](https://multiqc.info/)
* **BamUtils** Jun, G., Wing, M. K., Abecasis, G. R., & Kang, H. M. (2015). An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data. Genome Research, 25(6), 918–925. [https://doi.org/10.1101/gr.176552.114](https://doi.org/10.1101/gr.176552.114) Download: [https://genome.sph.umich.edu/wiki/BamUtil](https://genome.sph.umich.edu/wiki/BamUtil)
* **FastP** Chen, S., Zhou, Y., Chen, Y., & Gu, J. (2018). fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics , 34(17), i884–i890. [https://doi.org/10.1093/bioinformatics/bty560](https://doi.org/10.1093/bioinformatics/bty560) Download: [https://github.com/OpenGene/fastp](https://github.com/OpenGene/fastp)