ESILs

The bash script is used for alignement of fastq files and preparing the list of Single Nucleotide Polymorphisms (SNPs) in a short genetic interval for a studied Arabidopsis cross. This is applied to sequenced libraries, coming from a long-range PCR, however it might be used for whole-genome-sequencing data with some modifications. Firstly, the paired-end reads are pooled and aligned to a reference sequence. Resulting bam file is sorted and indexed. Later samtools mpileup and bcftools are used to prepare a .txt extension list of all the SNPs found in a studied DNA sequence. Similarly, individual paired-end fastq files are aligned to the reference sequence and later a list of SNPs with number of reads per each SNP is produced. The R script is used to filter out the SNPs found in the individuals, assign a genotype and visualize the data. Script was prepared by Wojciech Dziegielewski, Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan.