MicroSEC: Sequence Error Filter for Formalin-Fixed and Paraffin-Embedded
Samples
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: |
2.1.3 |
| 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: |
2024-07-26 |
| DOI: |
10.32614/CRAN.package.MicroSEC |
| Author: |
Masachika Ikegami [aut, cre] |
| Maintainer: |
Masachika Ikegami <ikegamitky at gmail.com> |
| BugReports: |
https://github.com/MANO-B/MicroSEC/issues |
| License: |
MIT + file LICENSE |
| URL: |
https://github.com/MANO-B/MicroSEC/ |
| NeedsCompilation: |
no |
| Language: |
en-US |
| Materials: |
README NEWS |
| CRAN checks: |
MicroSEC results |
Documentation:
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