ab1-fastq.pl for reading ABI Sanger sequencing trace file, and simulating the primarySeq and secondarySeq to fastq reads by extracting 90 bp blocks from Sanger sequence and shifting 1-bp in turns. As an example, a 200 bp Sanger sequence would obtain 110 fastq reads within the length of 90 bp.
ab1-fastq.pl is from CandiHap Sanger_ab1: https://github.com/xukaili/CandiHap
perl 5, R ≥ 3.2 (with sangerseqR).
install sangerseqR packages in R:
if (! requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
if (! require("sangerseqR")) BiocManager::install("sangerseqR")
Put sanger_CandiHap.sh, Gene_VCF2haplotypes.pl, ab1-fastq.pl and all sanger_teat_data files in a same dir, then run:
perl ab1-fastq.pl Sanger.ab1
e.g. perl ab1-fastq.pl example_F.ab1
Academic users may download and use the application free of charge according to the accompanying license. Commercial users must obtain a commercial license from Xukai Li. If you have used the program to obtain results, please cite the following paper:
Xukai Li☯* (李旭凯), Zhiyong Shi☯ (石志勇), Qianru Qie (郄倩茹), Jianhua Gao (高建华), Yiwei Jiang (姜亦巍), Yuanhuai Han (韩渊怀) & Xingchun Wang* (王兴春). CandiHap: a haplotype analysis toolkit for natural variation study. bioRxiv 2020.02.27.967539. doi: https://doi.org/10.1101/2020.02.27.967539
（☯ Equal contributors; * Correspondence）