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

In CrispRVariants: Tools for counting and visualising mutations in a target location

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

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

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.