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dupsifter

dupsifter is a command line tool for marking PCR duplicates in both WGS and WGBS datasets. It is based on the samblaster methodology for finding and marking duplicates.

Publication

If you use dupsifter, kindly cite:

Jacob Morrison, Wanding Zhou, Benjamin K Johnson, Hui Shen,
Dupsifter: a lightweight duplicate marking tool for whole genome bisulfite sequencing,
Bioinformatics, Volume 39, Issue 12, December 2023, btad729,
https://doi.org/10.1093/bioinformatics/btad729

Documentation

Documentation, including installation and usage, can be found in the docs/ directory and at https://huishenlab.github.io/dupsifter/.

Download and Install

All releases are available on GitHub.

Specifics about installation can be found in docs/install.qmd or on the documentation site.

Examples

Examples of using dupsifter can be found in docs/examples.qmd or on the documentation site. Test data can be found in the example directory.

Issues

Issues and bugs can be submitted to: https://github.com/huishenlab/dupsifter/issues.

Acknowledgments

  • This work is based on Gregory Faust's samblaster.
  • This work is supported by NIH/NCI R37CA230748.