Highlights for the 5.0.0 version
• Fast analysis of complete big panels (like Whole Exome Sequencing)
• Easy and fast definition of big panels without creating ROIs
• Import of gene lists for filtering and analysis of WES data for step-by-step diagnostic
• CNV analysis for patients analysed for different genes with the same panel as reference
• Aneuploidy analysis
• realignment for detection of internal tandem duplications (e.g for the FLT3 gene)
• Improved analysis of UMIs
General features of SEQNEXT
• Compatible with data produced by all main next-generation platforms and kits
• Easy set up of ROIs for individual genes, gene-panels and larger sets of genes via import of bed- or manifest-files based on hg19 and/or hg38
• Analysis of fastq, fastq.gz- or bam-files
• Efficient standards for mapping, alignment, quality and variant calling (used algorithms: BWA and Smith-Waterman, adapted by JSI)
• Personalized settings for analysis and variant calling (≥ 0.1 %)
• Adjustable settings such as whole genome mapping to filter pseudogene and homology background
• High sensitivity and specificity for detection of SNPs, deletions and insertions of any length, as well as CNVs and gene fusions
• Easy change of transcript in the analysis view
• Analysis of FFPE samples and molecular tagged sequences (e.g. smMIPs, UMIs)
• Patient identification and genotyping via SNP IDs
• All results for one patient are shown on one screen incl. found mutations / variations, amino acid changes, HGVS nomenclatures etc.
• Public SNP-databases dbSNP, 1000 Genomes, EXAC, gnomAD and ClinVar are available for individual display and filter functions
• Warnings for low quality, low coverage, no base calling and drop-outs
• Detailed summary of coverage and quality and information about "unused reads"
• Result export in vcf-file format (automatic with our TALKMASTER module)
• Internal mutation database keeping track of mutation detection history from SEQNEXT and SEQPATIENT (SeqPilot Sanger module)
• Detailed sequencing report for individual patients/orders
• Manual or automatic transfer of all detected variants into varSEAK local for further filtering, interpretation and report
