Services Bioinformatics
Overview Illumina sequencing Sample preparation Bioanalyzer Qubit 3.0 fluorometer Bioinformatics Service Price
  • Quality control and experimental variables assessment (trimming and cleaning)
    •De-multiplexing •Quality-based and adapter trimming •Removal of artifacts, homopolymers •Assess the difference in the quality and quantity between the libraries and replicates in the same experiments •Assess the difference between libraries sequenced on different lanes, flowcells or platforms •Assess the difference between the different kinds of libraries
  • Read mapping to a reference genome
    This is only the mapping component and includes: •Testing different mapping algorithms and selection of the best one for the particular data set. •Optimization of the mapping parameters. •Generation of mapping files in a common format, e.g. SAM/BAM. •Generation of files for mapped and un-mapped reads.
  • Mapping to a reference for transcriptome assembly
    Transcriptome reference assembly (mapping, clustering and exporting consensus transcript sequences). Testing of different mapping algorithms and selection of the best for the particular data set. •Optimization of the mapping parameters. •Generation of mapping files in a common format – Generation of files for mapped and un-mapped reads. •Generation of a sequence file containing the assembled sequences.
  • Mapping to a reference transcriptome(s) for transcriptional analysis
    This is mapping to a reference for gene expression profiling and isoform detection. Testing different mapping algorithms and selection of the best for the particular data set. •Optimization of the mapping parameters. •Generation of mapping files in a common format. •Generation of files for mapped and un-mapped reads. •Generation of counts (RPM, RPKM, or FBKM) file per each replicate, condition, sample, and experiment. •Generation of a new isoforms file (only if a nicely annotated reference is available).
  • De novo genome assembly
    •Assembly of contigs/scaffolds. •Statistical assessment of the assembly. •Comparison to public database or other reference. •Assessment of the ortholog gene regions (benchmarks).
  • De novo transcriptome assembly
    •Assemble using different k-mers and select the best range of k-mers. •Re-assemble using overlapping-based method. •Generate contigs/scaffolds. •Statistical assessment of the assembly. •Comparison to public databases (mRNA and protein). •Assessment of the ortholog gene regions (benchmarks).
  • Transcriptome annotation
    •Reciprocal BLAST to nucleotide and protein database. •Parsing the results. •Generation of a spreadsheet for the gene description.
  • Differential expression analysis
    •Assuming reads are already mapped and available in “SAM” or “BAM” format.
  • SNPs detection/calling/filtering
    •Assuming reads are already mapped and available in “SAM” or “BAM” format.
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