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Correctly counting molecules using unique molecular identifiers (UMIs)

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Description

Motivation: Counting molecules using next-generation sequencing (NGS) suffers from PCR amplification bias, which reduces the accuracy of many quantitative NGS-based experimental methods such as RNA-Seq. This is true even if molecules are made distinguishable using unique molecular identifiers (UMIs) before PCR amplification, and distinct UMIs are counted instead of reads: Molecules that are lost entirely during the sequencing process will still cause under-estimation of the molecule count, and amplification artifacts like PCR chimeras create phantom UMIs and thus cause over-estimation.

Results: TRUmiCount uses a mechanistic model of PCR amplification to correct for both types of errors. In our paper (see below) we demonstrate that the phantom-filtered and loss-corrected molecule counts computed by TRUmiCount measure the true number of molecules with considerably higher accuracy than the raw number of distinct UMIs.

Availability

TRUmiCount is available on the Bioconda channel of the Conda package manager.

conda install -c bioconda trumicount

More Information

See https://cibiv.github.io/trumicount for detailes on the installation & usage of TRUmiCount.

The TRUmiCount algorithmus and our model of PCR amplification and sequencing is described in details in our paper:

Florian G. Pflug, Arndt von Haeseler. (2018). TRUmiCount: Correctly counting absolute numbers of molecules using unique molecular identifiers. Bioinformatics, DOI: https://doi.org/10.1093/bioinformatics/bty283.

License

TRUmiCount is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

TRUmiCount is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.