Installing

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BiocManager::install(“Biostrings”)

Libraries

library(rentrez)

library(genbankr)

library(DECIPHER)

library(ggtree)

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Biostrings

unlist() # coallates multiple elements into a single sequence.

Length()

width() # number of characters per sequence, used in sets.

complement() # produces a complement strand.

rev() #changes sequence order from top to bottom..

reverse(). # changes order from left to right 2

reverseComplement() # reverses the complement of the sequence.

subseq() # subset 1 or more sequences from an existing sequence.

SHORT Reads

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readFasta()

readFastq()

writeFastq()

set.seed()

alphabetByCycle() # letter frequencies per cycle.

sread() # extract sequence from short read object

class() # check class of sample.

quality() # check quality of sequence, given in encoding values.

PhredQuality() # transform encoding values of quality.

yeild() # extracts information from stored file.

methods(class = “ShortRead”) # methods accessors for fasta.

methods(class = “ShortReadQ”) # methods accessors for fastq.

polynFilter() #selects reads that contain less than the given number of duplicate nucleotides.