BSREx-seq analysis tool

Shangang Jia, Chi Zhang, and David Holding

BSREx-seq (Bulked Segregant RNA and Exome sequencing) enables the complete analysis of BSR-seq (Bulked Segregant RNA-seq) and exome-seq (exome sequencing), by calling the thrid party softwares, including Samtools, Bowtie2 and VarScan. It is an integrated pipeline from input of raw fastq data, alignment, SNPs/indel calling, identifying deleted exons, and plotting mapping linkage peaks and deleted exons. It supports inputs of fastq or bam files in a comparison of normal type and mutant type in BSR-seq for F2 generation, and normal type and mutant type in exome-seq for Mxx generation. This script has a flexibility to process BSR-seq or exome-seq data, and generates the results in one command line.

Download: - BSREx-seq analysis tool

This file contains the source code of BSREx-seq analysis tool and instruction for users, including installation and application.

GPPD (Genomic PCR Primer Designer) enables the automatic primer design for causal deletions, and other mutations, including SNPs and small indel, by calling the Primer3 and BLAST. It is originally written in Perl to verify the causal deletion and gene candidates by BSRE, but it can be extended in other uses, which needs plenty of primers and don't want to do it manually.

Download: - GPPD

This file contains the source code of Genomic PCR Primer Designer and instruction for users, including installation and application.

Please cite us if you use any of these material.

Please address questions or comments to czhang5@unl.edu .