sep_assem | R Documentation |
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 )
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)
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