abifToFastq {CrispRVariants} | R Documentation |
This is an R implementation of Wibowo Arindrarto's abifpy.py trimming module, which itself implement's Richard Mott's trimming algorithm See https://github.com/bow/abifpy for more details.
abifToFastq(seqname, fname, outfname, trim = TRUE, cutoff = 0.05, min_seq_len = 20, offset = 33, recall = FALSE)
seqname |
name of sequence, to appear in fastq file |
fname |
filename of sequence in ab1 format |
outfname |
filename to append the fastq output to |
trim |
should low quality bases be trimmed from the ends? TRUE or FALSE |
cutoff |
probability cutoff |
min_seq_len |
minimum number of sequenced bases required in order to trim the read |
offset |
phred offset for quality scores |
recall |
Use sangerseqR to resolve the primary sequence if two sequences are present. May cause quality scores to be ignored. (Default: FALSE) |
Requires Bioconductor package SangerseqR
None. Sequences are appended to the outfname.
Helen Lindsay
ab1_fname <- system.file("extdata", "IM2033.ab1", package = "CrispRVariants") abifToFastq("IM2033", ab1_fname, "IM2033.fastq")