abifToFastq {CrispRVariants} | R Documentation

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

### 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")

[Package CrispRVariants version 1.8.0 Index]