Blog Series: WoG, Cesky Krumlov; Day 5: Short Read Alignment

I found myself attempting to remember what day it was today...apparently lots of attendees including myself are losing track of the days. One thing we never lose track of though is the bar...and heading to it for a few beers/drinks after the 7-10pm session...cheers.

Dr. Konrad Paszkiewicz
University of Exeter

Topic: Short Read Alignment

In general short read alignments are difficult because the shorter your read the less likely it is to match uniquely to a given reference or sequence of interest. Instead it'll match to multiple places and you won't be sure exactly where it goes.

Ok, so if it's difficult to align short reads, why do people generate them? Well for one it's cheaper. Additionally, for many applications a short read of about 50 bp is enough to work with; for example resequencing of small organisms, de novo analysis of bacterial genomes which are usually quite small compared to a human genome, ChIP-seq or digital gene expression.