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Rsolid is an R package for normalizing fluorescent intensity data from ABI/SOLiD second generation sequencing platform. It has been observed that the color-calls provided by factory software contain technical artifacts, where the proportions of colors called are extremely variable across sequencing cycles. Under the random DNA fragmentation assumption, these proportions should be equal across sequencing cycles and proportional to the dinucleotide frequencies of the sample. Rsolid implements a version of the quantile normalization algorithm that transforms the intensity values before calling colors. Results show that after normalization, the total number of mappable reads increases by around 5%, and number of perfectly mapped reads increases by 10%. Moreover a 2-5% reduction in overall error rates is observed, with a 2-6% reduction in the rate of valid adjacent color mis-matches. The latter is important, since it leads to a decrease in false-positive SNP calls. The normalization algorithm is computationally efficient. In a test we are able to process 300 million reads in 2 hours using 10 computer cluster nodes. The engine functions of the package are written in C for better performance.
| Package | Summary | Distribution | Download |
| R-Rsolid-0.9.31-48.fc41.aarch64.html | Quantile normalization and base calling for second generation sequencing data | Fedora Rawhide for aarch64 | R-Rsolid-0.9.31-48.fc41.aarch64.rpm |
| R-Rsolid-0.9.31-48.fc41.i686.html | Quantile normalization and base calling for second generation sequencing data | Fedora Rawhide for x86_64 | R-Rsolid-0.9.31-48.fc41.i686.rpm |
| R-Rsolid-0.9.31-48.fc41.ppc64le.html | Quantile normalization and base calling for second generation sequencing data | Fedora Rawhide for ppc64le | R-Rsolid-0.9.31-48.fc41.ppc64le.rpm |
| R-Rsolid-0.9.31-48.fc41.s390x.html | Quantile normalization and base calling for second generation sequencing data | Fedora Rawhide for s390x | R-Rsolid-0.9.31-48.fc41.s390x.rpm |
| R-Rsolid-0.9.31-48.fc41.x86_64.html | Quantile normalization and base calling for second generation sequencing data | Fedora Rawhide for x86_64 | R-Rsolid-0.9.31-48.fc41.x86_64.rpm |
| R-Rsolid-0.9.31-48.fc40.aarch64.html | Quantile normalization and base calling for second generation sequencing data | Fedora 40 updates for aarch64 | R-Rsolid-0.9.31-48.fc40.aarch64.rpm |
| R-Rsolid-0.9.31-48.fc40.i686.html | Quantile normalization and base calling for second generation sequencing data | Fedora 40 updates for x86_64 | R-Rsolid-0.9.31-48.fc40.i686.rpm |
| R-Rsolid-0.9.31-48.fc40.x86_64.html | Quantile normalization and base calling for second generation sequencing data | Fedora 40 updates for x86_64 | R-Rsolid-0.9.31-48.fc40.x86_64.rpm |
| R-Rsolid-0.9.31-46.fc40.aarch64.html | Quantile normalization and base calling for second generation sequencing data | Fedora 40 for aarch64 | R-Rsolid-0.9.31-46.fc40.aarch64.rpm |
| R-Rsolid-0.9.31-46.fc40.i686.html | Quantile normalization and base calling for second generation sequencing data | Fedora 40 for x86_64 | R-Rsolid-0.9.31-46.fc40.i686.rpm |
| R-Rsolid-0.9.31-46.fc40.ppc64le.html | Quantile normalization and base calling for second generation sequencing data | Fedora 40 for ppc64le | R-Rsolid-0.9.31-46.fc40.ppc64le.rpm |
| R-Rsolid-0.9.31-46.fc40.s390x.html | Quantile normalization and base calling for second generation sequencing data | Fedora 40 for s390x | R-Rsolid-0.9.31-46.fc40.s390x.rpm |
| R-Rsolid-0.9.31-46.fc40.x86_64.html | Quantile normalization and base calling for second generation sequencing data | Fedora 40 for x86_64 | R-Rsolid-0.9.31-46.fc40.x86_64.rpm |
| R-Rsolid-0.9.31-44.fc39.aarch64.html | Quantile normalization and base calling for second generation sequencing data | Fedora 39 for aarch64 | R-Rsolid-0.9.31-44.fc39.aarch64.rpm |
| R-Rsolid-0.9.31-44.fc39.i686.html | Quantile normalization and base calling for second generation sequencing data | Fedora 39 for x86_64 | R-Rsolid-0.9.31-44.fc39.i686.rpm |
| R-Rsolid-0.9.31-44.fc39.ppc64le.html | Quantile normalization and base calling for second generation sequencing data | Fedora 39 for ppc64le | R-Rsolid-0.9.31-44.fc39.ppc64le.rpm |
| R-Rsolid-0.9.31-44.fc39.s390x.html | Quantile normalization and base calling for second generation sequencing data | Fedora 39 for s390x | R-Rsolid-0.9.31-44.fc39.s390x.rpm |
| R-Rsolid-0.9.31-44.fc39.x86_64.html | Quantile normalization and base calling for second generation sequencing data | Fedora 39 for x86_64 | R-Rsolid-0.9.31-44.fc39.x86_64.rpm |
| R-Rsolid-0.9.31-42.fc38.aarch64.html | Quantile normalization and base calling for second generation sequencing data | Fedora 38 updates for aarch64 | R-Rsolid-0.9.31-42.fc38.aarch64.rpm |
| R-Rsolid-0.9.31-42.fc38.i686.html | Quantile normalization and base calling for second generation sequencing data | Fedora 38 updates for x86_64 | R-Rsolid-0.9.31-42.fc38.i686.rpm |
| R-Rsolid-0.9.31-42.fc38.x86_64.html | Quantile normalization and base calling for second generation sequencing data | Fedora 38 updates for x86_64 | R-Rsolid-0.9.31-42.fc38.x86_64.rpm |
| R-Rsolid-0.9.31-41.fc38.aarch64.html | Quantile normalization and base calling for second generation sequencing data | Fedora 38 for aarch64 | R-Rsolid-0.9.31-41.fc38.aarch64.rpm |
| R-Rsolid-0.9.31-41.fc38.i686.html | Quantile normalization and base calling for second generation sequencing data | Fedora 38 for x86_64 | R-Rsolid-0.9.31-41.fc38.i686.rpm |
| R-Rsolid-0.9.31-41.fc38.ppc64le.html | Quantile normalization and base calling for second generation sequencing data | Fedora 38 for ppc64le | R-Rsolid-0.9.31-41.fc38.ppc64le.rpm |
| R-Rsolid-0.9.31-41.fc38.s390x.html | Quantile normalization and base calling for second generation sequencing data | Fedora 38 for s390x | R-Rsolid-0.9.31-41.fc38.s390x.rpm |
| R-Rsolid-0.9.31-41.fc38.x86_64.html | Quantile normalization and base calling for second generation sequencing data | Fedora 38 for x86_64 | R-Rsolid-0.9.31-41.fc38.x86_64.rpm |
| R-Rsolid-0.9.31-40.fc37.aarch64.html | Quantile normalization and base calling for second generation sequencing data | Fedora 37 testing updates for aarch64 | R-Rsolid-0.9.31-40.fc37.aarch64.rpm |
| R-Rsolid-0.9.31-40.fc37.aarch64.html | Quantile normalization and base calling for second generation sequencing data | Fedora 37 for aarch64 | R-Rsolid-0.9.31-40.fc37.aarch64.rpm |
| R-Rsolid-0.9.31-40.fc37.i686.html | Quantile normalization and base calling for second generation sequencing data | Fedora 37 testing updates for x86_64 | R-Rsolid-0.9.31-40.fc37.i686.rpm |
| R-Rsolid-0.9.31-40.fc37.i686.html | Quantile normalization and base calling for second generation sequencing data | Fedora 37 for x86_64 | R-Rsolid-0.9.31-40.fc37.i686.rpm |
| R-Rsolid-0.9.31-40.fc37.ppc64le.html | Quantile normalization and base calling for second generation sequencing data | Fedora 37 for ppc64le | R-Rsolid-0.9.31-40.fc37.ppc64le.rpm |
| R-Rsolid-0.9.31-40.fc37.s390x.html | Quantile normalization and base calling for second generation sequencing data | Fedora 37 for s390x | R-Rsolid-0.9.31-40.fc37.s390x.rpm |
| R-Rsolid-0.9.31-40.fc37.x86_64.html | Quantile normalization and base calling for second generation sequencing data | Fedora 37 testing updates for x86_64 | R-Rsolid-0.9.31-40.fc37.x86_64.rpm |
| R-Rsolid-0.9.31-40.fc37.x86_64.html | Quantile normalization and base calling for second generation sequencing data | Fedora 37 for x86_64 | R-Rsolid-0.9.31-40.fc37.x86_64.rpm |
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