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AI & Computer Vision: UFMFEV-30-M: Genome Sequencing
AI & Computer Vision: UFMFEV-30-M: Genome Sequencing
Vision
UFMFEV-30-M: Genome Sequencing
Overview
• High Throughput Sequencing Technologies
• 454
• IonTorrent
• Illumina
• PacBio
• Oxford Nanopore
• Sequencing Data and Assembly
• Reads
• De novo and reference-based assembly
https://www.genome.gov/about-genomics/fact-sheets/DNA-Sequencing-Costs-Data
• Pyrosequencing
ACCTTGAGTACCATCTAGGA---------
AGATCCT---------
• Polymerase
dATP PPi
ATP-Sulfurylase
• ATP-Sulfurylase ATP
Luciferase
• Luciferase Light
Adaptor
Primer
/1 read /2 read
@HWI-D00151:214:HYFTWADXX:1:1101:2002:2201 1:N:0:CAGAGAGGTATCCTCT
GCTCTACACGGTAGTAAACACGACGAGGCACACCCATCTTTTTTTCAGAG
+
8BB;FFFFFFFFFIFII@I=II…-&-&-*,,,,,IIIIIIIIIFFFFFFFFFFFFFFFF Sequence
Separator Line
Encoded quality values, one
symbol per nucleotide
!”#$%&’()*+,-./0123456789::;<=>?@ABCDEFGHIJ
Adaptor Clipping
• Align 3’ and 5’ ends of reads against all adaptor sequences
• If a match is found, the read is trimmed
Scaffolds
De novo assembly
• De novo assembly is the process of reconstructing the original DNA sequence
using only the read sequences
• Like a jigsaw puzzle
• Involves finding overlaps between reads
• Sequencing errors can impair our ability to do this