Analyze_Sangers: Preprocessing and annotation of Sanger sequencing of the 16S...

In CMET-UGent/CMETNGS: Convenience functions for CMET NGS automated pipeline

Description

Preprocessing and annotation of Sanger sequencing of the 16S rRNA gene

Usage

Analyze_Sangers(
  inputfile = NULL,
  inputfolder = NULL,
  fwd_suffix = "F",
  rev_suffix = "R",
  primerFname = "27F",
  primerRname = "1492R",
  fastas_only = FALSE,
  resfolder = "Results",
  verbose = FALSE,
  trim.cutoff = 0.005,
  ncores = 2,
  mintrim = 300L,
  ...
)

Arguments

inputfile	LGC text file containing forward and reversed reads
inputfolder	folder containing the ab1 files with the raw spectrograms from an ABI capillary electrophoresis instrument. only used when raw=TRUE (currently defunct, but should be easy to implement if there is need)
fwd_suffix	string containing the suffix of the forward reads (defaults to F)
rev_suffix	string containing the suffix of the reverse reads (defaults to R)
primerFname	string containting the (abbreviated) name of the forward primer (like it occurs in the fasta file, defaults to 27F)
primerRname	string containting the (abbreviated) name of the reverse primer (like it occurs in the fasta file, defaults to 27F)
fastas_only	if you do not want merging to occur but want separate fasta files to be spitted out for downstream processing in e.g. BioEdit. ( defaults to FALSE)
resfolder	name of the folder to put the results in (defaults to "Results/")
verbose	print out progress (defaults to FALSE)
trim.cutoff	sangeranalyseR::summarise.abi.folder argument (defaults to 5e-3)
ncores	number of cores for sangeranalyseR::summarise.abi.folder ( defaults to 2, and will be set to 1 on windows)
mintrim	minimal length of trimmed reads in the folder workflow to retain before merging (defaults to 300)
...	additional arguments passed on to BioStrings::readDNAStringSet or sangeranalyseR::summarise.abi.folder in case inputfile==NULL and inputfolder is specified

Value

either a list of the consensus reads, forward and reverse reads or a summarised abi folder

Examples

##File-based workflow (LGC-preprocessed)

fastademoset <- system.file("extdata","sanger_demodata.txt",
                              package = "CMETNGS",mustWork = TRUE)
consensusres   <- Analyze_Sangers(inputfile=fastademoset,fwd_suffix="F",
                                  rev_suffix="R",primerFname="27F",
                                  primerRname="1492R",verbose=TRUE)
##File-based workflow for DSP in BioEdit

fastares   <- Analyze_Sangers(inputfile=fastademoset,fwd_suffix="F",
                               rev_suffix="R",fastas_only=TRUE)
##Folder-based workflow

# TODO: find proper example set

CMET-UGent/CMETNGS documentation built on Dec. 12, 2020, 8:22 a.m.