Description
Variant determination and genotyping from high throughput sequences from multilocus amplicon libraries, typically sequenced in Illumina MiSeq or similar. It provides a set of core functions for the central steps: demultiplex by locus, truncate reads, variant calling, and genotype calling. Additionally, it provides a set of functions for diagnosis and estimation of best running parameters and multiple extensions for genotype/variants manipulation and reformatting. Output variants and genotypes are output in 'tidy' format, thus facilitating reformatting, manipulation and potential connection to other R packages.
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Show all 14 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | ERROR |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | ERROR |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | ERROR |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check details (14 non-OK)
package dependencies
Packages required but not available: 'Biostrings', 'dada2', 'ShortRead', 'DECIPHER' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
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package dependencies
Packages required but not available: 'dada2', 'ShortRead', 'DECIPHER' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
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package dependencies
Packages required but not available: 'dada2', 'DECIPHER' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
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Check History
ERROR 11 OK · 0 NOTE · 0 WARNING · 3 ERROR · 0 FAILURE Mar 9, 2026
package dependencies
Packages required but not available: 'Biostrings', 'dada2', 'ShortRead', 'DECIPHER' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Packages required but not available: 'dada2', 'DECIPHER' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
package dependencies
Packages required but not available: 'dada2', 'ShortRead', 'DECIPHER' See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.