title: QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species.
abstract: BACKGROUND
  Single nucleotide polymorphisms (SNPs) are important tools in studying complex genetic traits and genome evolution. Computational strategies for SNP discovery make use of the large number of sequences present in public databases (in most cases as expressed sequence tags (ESTs)) and are considered to be faster and more cost-effective than experimental procedures. A major challenge in computational SNP discovery is distinguishing allelic variation from sequence variation between paralogous sequences, in addition to recognizing sequencing errors. For the majority of the public EST sequences, trace or quality files are lacking which makes detection of reliable SNPs even more difficult because it has to rely on sequence comparisons only.
  
  
  RESULTS
  We have developed a new algorithm to detect reliable SNPs and insertions/deletions (indels) in EST data, both with and without quality files. Implemented in a pipeline called QualitySNP, it uses three filters for the identification of reliable SNPs. Filter 1 screens for all potential SNPs and identifies variation between or within genotypes. Filter 2 is the core filter that uses a haplotype-based strategy to detect reliable SNPs. Clusters with potential paralogs as well as false SNPs caused by sequencing errors are identified. Filter 3 screens SNPs by calculating a confidence score, based upon sequence redundancy and quality. Non-synonymous SNPs are subsequently identified by detecting open reading frames of consensus sequences (contigs) with SNPs. The pipeline includes a data storage and retrieval system for haplotypes, SNPs and alignments. QualitySNP's versatility is demonstrated by the identification of SNPs in EST datasets from potato, chicken and humans.
  
  
  CONCLUSIONS
  QualitySNP is an efficient tool for SNP detection, storage and retrieval in diploid as well as polyploid species. It is available for running on Linux or UNIX systems. The program, test data, and user manual are available at http://www.bioinformatics.nl/tools/snpweb/ and as Additional files.
authors.affiliation: Plant Research International, PO Box 16, 6700 AA Wageningen, The Netherlands. jifeng.tang@wur.nl
authors.forename: Jifeng
authors.initials: J
authors.lastname: Tang
authors.forename: Ben
authors.initials: B
authors.lastname: Vosman
authors.forename: Roeland E
authors.initials: RE
authors.lastname: Voorrips
authors.forename: C Gerard
authors.initials: CG
authors.lastname: van der Linden
authors.forename: Jack A M
authors.initials: JA
authors.lastname: Leunissen
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D004252:DNA Mutational Analysis / Q000379:methods*; D004251:DNA Transposable Elements / Q000235:genetics*; D030541:Databases, Genetic; D004171:Diploidy; D020224:Expressed Sequence Tags; D017353:Gene Deletion; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011123:Polyploidy; D012984:Software
chemical_list: D004251:DNA Transposable Elements