| Type: | Package |
| Title: | Assembling Long Gene Copies from Short Read Data |
| Version: | 1.2.0 |
| Author: | Lei Yang |
| Maintainer: | Lei Yang <leiyangslu@gmail.com> |
| Description: | Assembles two or more gene copies from short-read Next-Generation Sequencing data. Works best when there are only two gene copies and read length >=250 base pairs. High and relatively even coverage are important. |
| License: | GPL-2 |
| URL: | https://github.com/LeiYang-Fish/copyseparator |
| BugReports: | https://github.com/LeiYang-Fish/copyseparator/issues |
| Depends: | R (≥ 3.5.0) |
| Encoding: | UTF-8 |
| Imports: | ape, seqinr, stringr, kmer, DECIPHER, beepr, Biostrings, grDevices, doParallel, foreach, parallel |
| RoxygenNote: | 7.2.1 |
| Suggests: | knitr, rmarkdown, testthat (≥ 3.0.0) |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2022-11-25 00:14:04 UTC; lyang1 |
| Repository: | CRAN |
| Date/Publication: | 2022-11-25 00:30:02 UTC |
copy_assemble
Description
Assembles a small number of overlapping DNA sequences into their respective gene copies.
Usage
copy_assemble(filename, copy_number, verbose = 1)
Arguments
filename |
A fasta alignment of a small number of overlapping DNA sequences (results from "copy_separate") covering the entire length of the target gene. Check the alignment carefully before proceeding. |
copy_number |
An integer (e.g. 2,3, or 4) giving the anticipated number of gene copies. Must be the same value as used for "copy_separate". |
verbose |
Turn on (verbose=1; default) or turn off (verbose=0) the output. |
Value
A fasta alignment of the anticipated number of full-length gene copies.
Examples
## Not run:
copy_assemble("inst/extdata/combined_con.fasta",2,1)
## End(Not run)
copy_detect
Description
Separates two or more gene copies from a single subset of short reads.
Usage
copy_detect(filename, copy_number, verbose = 1)
Arguments
filename |
A fasta file contains short reads from a single subset generated by "subset_downsize". |
copy_number |
An integer (e.g. 2,3, or 4) giving the anticipated number of gene copies in the input file. |
verbose |
Turn on (verbose=1; default) or turn off (verbose=0) the output. |
Value
A fasta alignment of the anticipated number of gene copies.
Examples
## Not run:
copy_detect("inst/extdata/toysubset.fasta",2,1)
## End(Not run)
copy_separate
Description
Separates two or more gene copies from short-read Next-Generation Sequencing data into a small number of overlapping DNA sequences.
Usage
copy_separate(
filename,
copy_number,
read_length,
overlap = 225,
rare_read = 10,
verbose = 1
)
Arguments
filename |
A fasta file contains thousands of short reads that have been mapped to a reference. The reference and reads that are not directly mapped to the reference need to be removed after mapping. |
copy_number |
An integer (e.g. 2,3, or 4) giving the anticipated number of gene copies in the input file. |
read_length |
An integer (e.g. 250, or 300) giving the read length of your Next-generation Sequencing data. This method is designed for read length >=250bp. |
overlap |
An integer describing number of base pairs of overlap between adjacent subsets. More overlap means more subsets. Default 225. |
rare_read |
A positive integer. During clustering analyses, clusters with less than this number of reads will be ignored. Default 10. |
verbose |
Turn on (verbose=1; default) or turn off (verbose=0) the output. |
Value
A fasta alignment of a small number of overlapping DNA sequences covering the entire length of the target gene. Gene copies can be assembled by reordering the alignment manually or use the function "copy_assemble".
Examples
## Not run:
copy_separate("inst/extdata/toydata.fasta",2,300,225,10,1)
## End(Not run)
copy_validate
Description
A tool to help identify incorrectly assembled chimeric sequences.
Usage
copy_validate(filename, copy_number, read_length, verbose = 1)
Arguments
filename |
A DNA alignment in fasta format that contains sequences of two or more gene copies (e.g. results from "copy_assemble"). |
copy_number |
An integer (e.g. 2,3, or 4) giving the number of gene copies in the input file. |
read_length |
An integer (e.g. 250, or 300) giving the read length of your Next-generation Sequencing data. |
verbose |
Turn on (verbose=1; default) or turn off (verbose=0) the output. |
Value
A histogram in pdf format showing the relationships between the physical distance between neighboring variable sites and read length.
Examples
## Not run:
copy_validate("inst/extdata/Final_two_copies.fasta",2,300,1)
## End(Not run)
sep_assem
Description
Separates two or more gene copies from short-read Next-Generation Sequencing data into a small number of overlapping DNA sequences and assemble them into their respective gene copies.
Usage
sep_assem(
copy_number,
read_length,
overlap = 225,
rare_read = 10,
core_number = 1,
verbose = 1
)
Arguments
copy_number |
An integer (e.g. 2,3, or 4) giving the anticipated number of gene copies in the input file. |
read_length |
An integer (e.g. 250, or 300) giving the read length of your Next-generation Sequencing data. This method is designed for read length >=250bp. |
overlap |
An integer describing number of base pairs of overlap between adjacent subsets. More overlap means more subsets. Default 225. |
rare_read |
A positive integer. During clustering analyses, clusters with less than this number of reads will be ignored. Default 10. |
core_number |
An integer describing number of cores to use. |
verbose |
Turn on (verbose=1; default) or turn off (verbose=0) the output. |
Value
A fasta alignment of the anticipated number of full-length gene copies.
Examples
## Not run:
sep_assem(2,300,225,10,1,1) # all input fasta files in the working directory will be processed
## End(Not run)
subset_downsize
Description
Subdivides the imported read alignment into subsets and then downsizes each subset by deleting those sequences that have too many gaps or missing data.
Usage
subset_downsize(filename, read_length, overlap, verbose = 1)
Arguments
filename |
A fasta file contains thousands of short reads that have been mapped to a reference. The reference and reads that are not directly mapped to the reference need to be removed after mapping. |
read_length |
An integer (e.g. 250, or 300) giving the read length of your Next-generation Sequencing data. This method is designed for read length >=250bp. |
overlap |
An integer describing number of base pairs of overlap between adjacent subsets. More overlap means more subsets. |
verbose |
Turn on (verbose=1; default) or turn off (verbose=0) the output. |
Value
A number of overlapping subsets (before and after downsizing) of the input alignment.
Examples
## Not run:
subset_downsize("inst/extdata/toydata.fasta",300,225,1)
## End(Not run)