NGS Prepaid Solution

Genome variant detection

• Variant analysis: detection and annotation of single nucleotide polymorphism (SNPs) and insertions and deletions (InDels)
• De novo genome assembly

Option 1:

• Sequence quality assessment
• Removal of poor quality bases, adapters, primers and others
• Taxonomic profiling using NCBI database of bacterial, archaeal fungal, protozoan and viral genomes
• Removal of host sequences (only applicable for human, mouse or rat samples)

Deliverables:

• FastQ Files (sequences and quality scores)
• Phylum, genus and species level OTU abundance tables (tsv) and graphs (png)
• Interactive species level OTU abundance plot (html)
• Species diversity indices (tsv) and plots (png)
• Rarefaction curves (png)

Option 2:

• Thorough assessment of sequence quality prior to metagenome annotation
• Removal of poor quality bases, adapters and primers
• Removal of host sequences
• Taxonomic profiling using established pre-built MiniKrakenDB constructed from complete bacterial, archaeal fungal, protozoan and viral genomes in RefSeq
• Screening for virulence factors and antibiotic resistance genes using MvirDB
• KEGG functional profiling of microbial communities using the integrated gene catalogue of the human gut microbiome (IGC)

Deliverables:

Taxonomic profiling

• FastQ Files (sequences and quality scores)
• Phylum, genus and species level OTU abundance tables (.tsv) and graphs (.png)
• Interactive species level OTU abundance plot (html)
• Species diversity indices (.tsv) and plots (.png)
• Rarefaction curves (.png)

Functional profiling

• KEGG annotation tables (.tsv) and graphs (.png)
• Correlation plots (.png)

Resistance profiling

• Antibiotic resistance and virulence tables (.tsv) and graphs (.png)
• Correlation plots (.png)

• Mapping against one reference
• Identification and quantification of transcripts
• Pairwise comparison (samples or groups of samples) of expression levels and determination of significant fold differences
• Principal Component Analysis (PCA)
• Alternative splicing analysis based on known/provided gene models for eukaryotes
• Fusion gene detection

Deliverables:

• Alignment file (bam)
• Gene expression table including FPKM value (tsv)
• Table of pair-wise differential expression including fold change and p-value (tsv)
• Combined gene expression table of all samples (tsv)
• Volcano plots (png)
• Tables of alternative splicing events (tsv)
• Table of fused transcripts/genes (tsv)
• Comprehensive Data Analysis Report (pdf)

Analysis

• Data sorting according to tags designed by Eurofins Genomics
• Data sorting according to customer supplied tag
• CRISPR mutation analysis

The CRISPR mutation analysis evaluates mutations introduced by non-homologous end joining (NHEJ) pathway. Our pipeline is designed for analysing events with single breaks.

• Quality clipping and merging of raw reads
• Mapping to target region(s) and quality filtering of mapped reads
• Clustering based identification and quantification of NHEJ events
• Quantification of mutation rates and of frameshift mutations
• For each sample and target region, detailed reporting of:
  • Wildtype and alternate allele sequences including quantification
  • Observed mutation rate plots, frameshift classification plots
  • Raw data, mapping, and coverage statistics

Deliverables

• Comprehensive report with results and methods sections
• Raw FASTQ files
• Quality clipped and assembled FASTQ files
• Mapped reads in BAM format (raw and filtered)
• Observed wildtype and alternate allele sequences including quantification
• Raw data, preprocessing, mapping, and coverage metrics in CSV format

• Pre-Processing of reads
• Chimera filtering
• Picking of OTU representative sequences (Operational Taxonomic Unit)
• Taxonomical assignment and read abundance estimation for all detected OTUs down to species level. Higher taxonomic ranks possible if assignment cannot be unambiguously resolved (e.g. at genus or family level). Specificity depends on starting material, taxonomic composition of sample, and availability of reference sequence in databases.
• Normalised abundance estimation of bacterial and arachaeal OTUs considering lineage-specific copy numbers of marker genes
• Microbial diversity analysis - alpha and beta diversity indices

Analysis deliverables:

• OTU composition tables (tsv)
• Graphical representation of taxonomic assignments (HTML)
• Microbial diversity tables (tsv)
• Comprehensive Data Analysis report (pdf)

1 Coupon per sample

• Mapping against one reference
• Detection of SNPs and InDels
• Annotation of detected SNPs and InDels (using dbSNP)
• Allocation of effects on protein level (using Ensembl)

Deliverables:

• Alignment file (bam)
• SNP and InDel tables including annotated variants and effects (vcf, tsv, bed)
• Comprehensive data analysis report (pdf)