| Title: | Assembling Long Gene Copies from Short Read Data |
|---|---|
| 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. |
| Authors: | Lei Yang |
| Maintainer: | Lei Yang <[email protected]> |
| License: | GPL-2 |
| Version: | 1.2.0 |
| Built: | 2024-10-30 05:16:42 UTC |
| Source: | https://github.com/leiyang-fish/copyseparator |
Assembles a small number of overlapping DNA sequences into their respective gene copies.
copy_assemble(filename, copy_number, verbose = 1)copy_assemble(filename, copy_number, verbose = 1)
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. |
A fasta alignment of the anticipated number of full-length gene copies.
## Not run: copy_assemble("inst/extdata/combined_con.fasta",2,1) ## End(Not run)## Not run: copy_assemble("inst/extdata/combined_con.fasta",2,1) ## End(Not run)
Separates two or more gene copies from a single subset of short reads.
copy_detect(filename, copy_number, verbose = 1)copy_detect(filename, copy_number, verbose = 1)
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. |
A fasta alignment of the anticipated number of gene copies.
## Not run: copy_detect("inst/extdata/toysubset.fasta",2,1) ## End(Not run)## Not run: copy_detect("inst/extdata/toysubset.fasta",2,1) ## End(Not run)
Separates two or more gene copies from short-read Next-Generation Sequencing data into a small number of overlapping DNA sequences.
copy_separate( filename, copy_number, read_length, overlap = 225, rare_read = 10, verbose = 1 )copy_separate( filename, copy_number, read_length, overlap = 225, rare_read = 10, verbose = 1 )
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. |
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".
## Not run: copy_separate("inst/extdata/toydata.fasta",2,300,225,10,1) ## End(Not run)## Not run: copy_separate("inst/extdata/toydata.fasta",2,300,225,10,1) ## End(Not run)
A tool to help identify incorrectly assembled chimeric sequences.
copy_validate(filename, copy_number, read_length, verbose = 1)copy_validate(filename, copy_number, read_length, verbose = 1)
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. |
A histogram in pdf format showing the relationships between the physical distance between neighboring variable sites and read length.
## Not run: copy_validate("inst/extdata/Final_two_copies.fasta",2,300,1) ## End(Not run)## Not run: copy_validate("inst/extdata/Final_two_copies.fasta",2,300,1) ## End(Not run)
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.
sep_assem( copy_number, read_length, overlap = 225, rare_read = 10, core_number = 1, verbose = 1 )sep_assem( copy_number, read_length, overlap = 225, rare_read = 10, core_number = 1, verbose = 1 )
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. |
A fasta alignment of the anticipated number of full-length gene copies.
## Not run: sep_assem(2,300,225,10,1,1) # all input fasta files in the working directory will be processed ## End(Not run)## Not run: sep_assem(2,300,225,10,1,1) # all input fasta files in the working directory will be processed ## End(Not run)
Subdivides the imported read alignment into subsets and then downsizes each subset by deleting those sequences that have too many gaps or missing data.
subset_downsize(filename, read_length, overlap, verbose = 1)subset_downsize(filename, read_length, overlap, verbose = 1)
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. |
A number of overlapping subsets (before and after downsizing) of the input alignment.
## Not run: subset_downsize("inst/extdata/toydata.fasta",300,225,1) ## End(Not run)## Not run: subset_downsize("inst/extdata/toydata.fasta",300,225,1) ## End(Not run)