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The results of metagenomic NGS can also be valuable even when concordant with results of conventional testing, not only providing reassurance that the conventionally obtained diagnosis is correct but also potentially detecting or ruling out coinfections, specially in immunocompromised patients. [9]
N50 statistic defines assembly quality in terms of contiguity.Given a set of contigs, the N50 is defined as the sequence length of the shortest contig at 50% of the total assembly length.
Schematic overview of the modular structure underlying procedures for gene set enrichment analysis. Gene set enrichment analysis (GSEA) (also called functional enrichment analysis or pathway enrichment analysis) is a method to identify classes of genes or proteins that are over-represented in a large set of genes or proteins, and may have an association with different phenotypes (e.g ...
SNV calling from NGS data is any of a range of methods for identifying the existence of single nucleotide variants (SNVs) from the results of next generation sequencing (NGS) experiments. These are computational techniques, and are in contrast to special experimental methods based on known population-wide single nucleotide polymorphisms (see ...
For the last read, the next read is the first read in the template. If @SQ header lines are present, RNEXT (if not ‘*’ or ‘=’) must be present in one of the SQ-SN tag. This field is set as ‘*’ when the information is unavailable, and set as ‘=’ if RNEXT is identical RNAME.
Long-read aligners (e.g. minimap2 [33]) often support chimeric alignment and can be directly applied to long-read Hi-C data. Short-read Hi-C alignment is more challenging. Notably, Hi-C generates ligation junctions of varying sizes, but the exact position of the ligation site is not measured.
Phred quality scores shown on a DNA sequence trace. A Phred quality score is a measure of the quality of the identification of the nucleobases generated by automated DNA sequencing.
GeneTalk is a web-based platform, tool, and database for filtering, reduction and prioritization of human sequence variants from next-generation sequencing (NGS) data. [1] [2] GeneTalk allows editing annotation about sequence variants and build up a crowd sourced database with clinically relevant information for diagnostics of genetic disorders.