Description: The service includes the processing of NGS data, including quality analysis, filtering and pre-processing of the data. Alignment, variants call (SNPs + indels and copy number variations), variants analysis and differential gene expression analysis.

Methodology: Reads quality analysis using FASTQC / FASTX-TOOLKIT, reads filtering using Trimmommatic or FASTX-TOOLKIT. Alignment with the reference genome (GRCh38 / hg38 or b37 / hg19) using BWA or Bowtie. Pre-processing and variants call using the GATK toolkit and in accordance with the good practices indicated by the Broad Institute. Variants analysis with Variant Effect Predictor or SnpEff. Differential expression analysis with Bioconductor packages.

Description: The service includes the processing NGS data, including quality analysis, filtering and pre-processing of the reads. Alignment with the reference genome, characterization of structural variants (SV), de novo assembly, assembly optimization, prediction and annotation of genes, search for coding genes or genomic regions of interest.

Methodology: Reads quality analysis using FASTQC / FASTX-TOOLKIT, reads filtering using Trimmommatic or FASTX-TOOLKIT. Different tools are used for de novo assembly (SPAdes, ABBySS, Flye, Unicycler) and also for the characterization of SVs (Lumpy, SvABA, Manta). To search for regions or genes of interest, the BLAST and HMMER tools are used, using databases associated to each particular requirement. Phylogenetic analysis based on ANI or genes of interest.

Description: The service includes the NGS data processing, including quality analysis, filtering and pre-processing of the reads, filtering of host reads, taxonomic classification of reads, assembly and prediction of genes.

Methodology: Reads quality analysis using FASTQC / FASTX-TOOLKIT, reads filtering using Trimmommatic or FASTX-TOOLKIT. The taxonomic profile is made with the Kaiju, Kraken or Centrifuge tools. The assembly is done with metaSPAdes, MEGAHIT. Binning analysis with the MetaBAT or CONCOCT tools.