Bioinformatics support

The Facility has a rich collection of analysis pipelines for various types of sequencing and expression array studies. Most of the components originate from established, publically available packages, complemented by several in-house developments.

  •  For expression array analysis we use Bioconductor and Limma.
  •  For general quality control of the sequencing experiments we use the FastQC package.
  •  For large scale mapping of short sequences to reference we use primarily BowTie2 and BWA For RNAseq experiments. For ChIPseq and FAIREseq experiments we also use BFAST For higher sensitivity. For small RNA and microRNA sequencing we use Shrimp2 and our in-house development MiMapper.
  •  For peak finding in ChIPSeq experiments we use CisGenome, MACS and Quest.
  •  For RNAseq analysis we use TopHat2, CuffLinks, DESeq2, edgeR and Trinity.
  •  For SNP and short indel detection we use the GATK toolkit, SAMTOOLS, FreeBayes and DINDEL.
  •  For denovo sequencing, the assemblers Velvet, AMOS and SOAPdenovo are avalaible.

We have developed an in-house experiment management system that integrates a web interface to all experimental and analysis data with the user session system of the UCSC genome browser. Using our local installation of the genome browser, all experimentations have web access both to the visualization tracks and all additional data.

B.S.R.C. "Alexander Fleming"
34 Fleming Street, 16672 Vari, Greece
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