abifToFastq: Read a file in ab1 (Sanger) format and convert to fastq

Description Usage Arguments Details Value Author(s) Examples

View source: R/abifToFastq.R

Description

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.

Usage

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abifToFastq(seqname, fname, outfname, trim = TRUE, cutoff = 0.05,
  min_seq_len = 20, offset = 33, recall = FALSE)

Arguments

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)

Details

Requires Bioconductor package SangerseqR

Value

None. Sequences are appended to the outfname.

Author(s)

Helen Lindsay

Examples

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ab1_fname <- system.file("extdata", "IM2033.ab1", package = "CrispRVariants")
abifToFastq("IM2033", ab1_fname, "IM2033.fastq")

Example output

Loading required package: ggplot2
Loading required namespace: sangerseqR
NULL
Warning message:
system call failed: Cannot allocate memory 

CrispRVariants documentation built on Nov. 8, 2020, 11:09 p.m.