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Ion Torrent sequencing: NGS technology based on the use of a semiconductor chip where the sample is loaded integrated with an ion-sensitive field-effect transistor able to sensitively detect reductions of the pH value due to the release of one or more protons after the incorporation of one or more dNTPs during sequencing by synthesis: the ...
</> (less-/greater-than sign) denotes a reference skip. This occurs, for example, if a base in the reference genome is intronic and a read maps to two flanking exons. If quality scores are given in a sixth column, they refer to the quality of the read and not the specific base.
Progressive alignment results are dependent on the choice of "most related" sequences and thus can be sensitive to inaccuracies in the initial pairwise alignments. Most progressive multiple sequence alignment methods additionally weight the sequences in the query set according to their relatedness, which reduces the likelihood of making a poor ...
Paired-end and long-read sequencing of the same sample can mitigate the deficits in short read sequencing by serving as a template or skeleton. Metrics to assess the quality of a de novo assembly include median contig length, number of contigs and N50. [66] RNA-Seq alignment with intron-split short reads.
FPGA based sliding window short read aligner which exploits the embarrassingly parallel property of short read alignment. Performance scales linearly with number of transistors on a chip (i.e. performance guaranteed to double with each iteration of Moore's Law without modification to algorithm).
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.
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.
NGS platforms Platform Template preparation Chemistry Max read length (bases) Run times (days) Max Gb per Run Roche 454 Clonal-emPCR Pyrosequencing 400‡ 0.42 0.40-0.60 GS FLX Titanium Clonal-emPCR Pyrosequencing 400‡ 0.42 0.035 Illumina MiSeq Clonal Bridge Amplification Reversible Dye Terminator 2x300 0.17-2.7 15 Illumina HiSeq