Hanan Begali Author

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A Pipeline for Markers Selection Using Restriction Site Associated DNA Sequencing (Radseq)

Author(s):

Hanan Begali

The discovery and assessment of genetic variants for Next Generation Sequencing (NGS), including Restriction site Associated DNA sequencing (RADSeq), is an important task in bioinformatics and comparative genetics. The genetic variants can be single-nucleotide polymorphisms (SNPs), insertions and deletions (Indels) when compared to a reference genome. Usually, the short reads are aligned to a reference genome at first using NGS alignment software, such as the Burrows- Wheeler Aligner (BWA). The alignment is usually stored into a BAM file, a binary format of standard SAM (Sequence Alignment/Map) protocol. Then analysis software, such as Genome analysis Toolkit (GATK) or SAMTools, together with scripts written in R programming language, could provide an efficient solution for calling vari... view more»

DOI: 10.4172/2329-9533.1000147

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