Citation: T. Schmutzer (2015-08-25): PreBreed Yield data processing scripts. DOI:10.5447/ipk/2015/7

Abstract: The developed scripts (FASTQ_splitter.pl and VCF_SNP_matrix_construction.pl) were developed to assist data processing in the PreBreed Yield project. FASTQ_splitter.pl: The Perl script assists to synchronize read pairs after quality trimming. Synchronization is required after quality trimming, in case the left or the right partner of a paired end or mate pair read was removed completely. Furthermore, it can be applied to split merged FASTQ files containing the first (R1) and the second (R2) read pair. VCF_SNP_matrix_construction.pl: The Perl script assists to read multiple VCF files and constructs a joint SNP matrix. It requires a list of VCF files, a PLIST file with positions of selected variant positions and a MPILEUP file with coverage information for each utilized read alignment.

License: CC BY 4.0 (Creative Commons Attribution)

DOI: 10.5447/ipk/2015/7

Content: 1 Directories 4 Files (27.7 KB)