What is the diff between sequence align and assembly?

[arkilis]

Newbie question.

As I played some bioinfo softwares, sometimes just get confused by the two words, do they mean the same thing?

Thanks,

[Apexy]

They are different. However, it has become very difficult to dissociate them because when attempting to achieve something involving one of them, it is unlikely to avoid the other. To me, this explains why a newbie may often come across both words in one writeup. To assembly, you will unavoidably need to align. This alignment may be:
-Reference guided- find overlapping paths between neighbouring reads that occur in a certain order after aligning them to a known sequence (usually a big one)
-De novo -find overlaps between reads or k-mers from reads to build a larger read

There are cases where you may align without explicitly attempting to build a larger sequence. This happens with SNP related tools such as BOWTIE.

Kindly read further to get a more concise picture.

I welcome any corrections to what I have just written.............

[bishwo]

In my understanding sequence alignment is aligning one or more sequences to know their similarity/difference and sequence assembly means creating longer sequence by aligning small sequence fragments.

[Apexy]

@ bishwo,
You are correct. Without diverting @arkilis, it is also possible to know the similarity between one or many sequences without explicitly aligning them as it is the case with tools that make use of alignment-free comparison statistic D2.

[lethalfang]

Newbie question.

As I played some bioinfo softwares, sometimes just get confused by the two words, do they mean the same thing?

Thanks,

Simply put, when you have a known reference sequence for an organism, you can align your sequence to that reference sequence, with the assumption that variations from the reference are rare.
On the other hand, assembly is required when no reference sequence is known.