How Hisat Works

Question

[XBria]

Hello everyone,

Can anyone of you please explain how hisat works? How it aligns the reads , how for long and short reads, whether all bases of a specific read are all within the exon area , or not then how it performs for each situation ? concordant or discordant etc .. Please briefly explain like you are teaching a kid ;)

An easy to understand reference is also appreciated !

Many thanks in advance.

Answer 1

[Matteo Schiavinato]

[rant mode] on: http://lmgtfy.com/?q=hisat2+documentation [\rant mode]

HISAT2 publication: https://www.nature.com/articles/nmeth.3317

[XBria]

I thought there might be some ppts explaining briefly (with figures) how it works. I have already checked those two you shared. anyway thanks.

[Matteo Schiavinato]

The way it works is basically the way most of the aligners works (I don't remember if smith-waterman or burrows-wheeler, one of the two).

If you go on Coursera, you'll find the NGS data analysis course held by Ben Langmead and all the Salzberg team, which is behind this software (and Bowtie, Cufflinks, Tophat, Ballgown, ...). Maybe that helps?

I don't think you'll find good ppt presentations about HISAT in particular, but you sure will find some about the two mentioned alignment algorithms.

[XBria]

Dear Macspider,

It is highly appreciated. I am gonna have a look at that.

Cheers

Answer 2

[h.mon]

Do you already understand the Burrows-Wheeler Transform? Not at child level, but two very good explanations:

http://spencer-carroll.com/an-easy-to-understand-explanation-of-the-burrows-wheeler-transform/

http://blog.thegrandlocus.com/2016/07/a-tutorial-on-burrows-wheeler-indexing-methods

http://blog.thegrandlocus.com/2017/05/a-tutorial-on-burrows-wheeler-indexing-methods-2

http://blog.thegrandlocus.com/2017/05/a-tutorial-on-burrows-wheeler-indexing-methods-3

Both have a simple example worked out step-by-step, and code implementing BWT.

[XBria]

It is great ! Many thanks