MicroSEC: Sequence Error Filter for Formalin-Fixed and Paraffin-Embedded Samples (original) (raw)
Clinical sequencing of tumor is usually performed on formalin-fixed and paraffin-embedded samples and have many sequencing errors. We found that the majority of these errors are detected in chimeric read caused by single-strand DNA with micro-homology. Our filtering pipeline focuses on the uneven distribution of the artifacts in each read and removes such errors in formalin-fixed and paraffin-embedded samples without over-eliminating the true mutations detected in fresh frozen samples.
Version: | 2.1.6 |
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Depends: | R (≥ 3.5.0) |
Imports: | stringr, dplyr, Biostrings, Rsamtools, GenomeInfoDb, BiocGenerics |
Suggests: | BSgenome.Hsapiens.UCSC.hg38, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 |
Published: | 2024-08-25 |
DOI: | 10.32614/CRAN.package.MicroSEC |
Author: | Masachika Ikegami [aut, cre] |
Maintainer: | Masachika Ikegami |
BugReports: | https://github.com/MANO-B/MicroSEC/issues |
License: | MIT + file |
URL: | https://github.com/MANO-B/MicroSEC/ |
NeedsCompilation: | no |
Language: | en-US |
Materials: | README NEWS |
CRAN checks: | MicroSEC results |
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