novoSNP3: Variant Detection and Sequence Annotation in Resequencing Projects

The same high-throughput techniques used to make genomic sequences generally available, are also useful in mapping the genetic differences between individuals. Resequencing of a genomic region in a set of individuals is considered the golden standard for the discovery of sequence variants. However, with the available high-throughput sequencing technology data analysis has become the rate-limiting step in data management and analysis of large resequencing projects. To solve this issue we developed a software package novoSNP that conscientiously discovers single nucleotide polymorphisms and insertion-deletion polymorphisms in sequence trace files in a fast, reliable and user friendly way. Furthermore, it can also be used to create databases containing annotated reference sequences, add and align trace data, keep track of validation status of variants, annotate variants, and produce reports on validated variants and genotypes. novoSNP is available from http://www.molgen.ua.ac.be/bioinfo/novosnp . There are versions for MS Windows as well as Linux