A solid quality-control analysis of AB solid short-read sequencing data

Research output: Contribution to journalArticlepeer-review


Next generation sequencers have greatly improved our ability to mine polymorphisms and mutations out of entire (or portions of) genomes. The reliability of their outputs, though, showed to be very related to the sequencing chemistry and to deeply affect the quality of the downstream analyses.We focus here on the two-base color code chemistry of AB SOLiD sequencers and propose a comprehensive quality controlmethodological and software pipeline. We used existing and custom tools to detect and purge short-reads of some common flaws due to sequencing errors and chemical hitches.We apply them to a cohort of SOLiD 4 runs and measure their joint efficacy in terms of the resulting ability to detect the greatest possible number of true variants.

Original languageEnglish
Article numberbbs048
Pages (from-to)684-695
Number of pages12
JournalBriefings in Bioinformatics
Issue number6
Publication statusPublished - Nov 2013


  • Genetics
  • Next generation sequencing
  • Sequencing quality control

ASJC Scopus subject areas

  • Molecular Biology
  • Information Systems


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