FinalistDx

Finalist Dx

FinalistDX is a powerful complete computing package designed for analysis of sequencing data produced by any of the Illumina NGS sequencing platforms such as low throughput systems MiniSeq and MiSeq as well as high- throughput NextSeq, HiSeq as well as NovaSeq. FinalistDX can also analyze data from any other sequencer that generate FASTQ files. FinalistDX consists of a desktop computer and analysis program running on Linux Operating System (Ubuntu 14.04 LTS). The software provides a friendly graphical user interface even for inexperienced users such as biologists or clinicians. FinalistDX is connected to the sequencer machine and serves at the same time as a backup server.

FinalistDX represents an integrated bioinformatics workflow which includes quality control, alignment, visualization, coverage analysis, variant calling, and variant annotation tools

Quality control

Generate quality control plots for evaluation of sequence runs at one click using popular open-source software FastQC. Users can check for sequencing quality before starting the alignment step.

Alignment

FinalistDX is designed to align reads ranging from 70 bp to 1 Mbp against a reference genome and supports split alignments. Human genomes hg19 and hg38 were selected as standard references. The alignment process is running in parallel using all available cores that make computation time very short.

Coverage quality analysis

Users can evaluate coverage in detail across all samples, looking at single-base coverage data. FinalistDX provides full information about base by base coverage for any selected region, minimum and maximum coverage, and automatically notifies if coverage falls under the threshold in any selected region or base. The software contains a predefined selection of BED files to limit the analysis and also supports the import of external BED files.

Variant calling

FinalistDX employs a robust statistic/heuristic algorithm for SNP/INDEL detection that meets desired thresholds for statistical significance, variant allele frequency, read depth and base quality

Variant annotation

FinalistDX gives variants a meaning based on annotation and additional identifiers on the level of nucleotides, proteins, transcripts, or genes. It enables users to select between Ensembl or RefSeq preinstalled off-line databases (hg19 and hg38) or to import their own databases. As an example, annotation can provide information about gene symbol, CCDS, protein identifier, Uniprot and dbSNP number, HGVS notation, exon/intron, codon, cds and strand orientation, transcript biotype, protein domains, SIFT and PolyPhen predictions, GMAF, identifies canonical transcripts, and many other.

Variant database

Annotated results in VCF files are stored in a searchable database in user-defined folders to easily find common and different variants according to the selected criteria (by coordinates, gene name, HGVS, rs number, and others).

Tools

FinalistDX can filter FASTQ files based on Phred quality score and supports adapter trimming, preventing low-quality bases and adapters to be included in the analysis.

Hardware specification

FinalistDX MINIMUM HARDWARE SPECIFICATION: Procesor: Intel Xeon E5-2620v2, 6 xcores (12 threads),12 x 2.4 GHz; HDD: 2 TB, 7200 RPM; SSD: 500 GB; Monitor: AOC 27”