molecular - basic bioinformatics

bioinformatics

using software and large data sets to gain a deeper understanding of biology

reference genome

published assembly of sequences of entire genome to which all other sequences are compared

hg38

current human reference genome, published in 2013

human reference genome

standard by which we determine if something is a variant

base calling (pre processing)

raw signal converted to raw read, throws out low quality reads and adapter sequences, spacers trimmed off, demultiplexing based on barcodes

variant calling

software finds locations of variance from reference at minimum threshold

shell (BASH) scripting

allows for sequential processing of NGS data without intervention

genome browsers

assists in contextualizing genomic information, multiple tracks of data can be viewed at once along whole genome

data growth problem

our ability to generate data is advancing faster than our ability to interpret it

small p large n problem

biological systems are too complex for humans to make accurate consistent assessments when using omics based methods