Starting to use BWA-SW

[miguelangel]

I would need to align sequences without any reference database (I have a database, but it is not aligned yet). My idea was to find some software that allows me to align this .fasta file and use it as an aligned database for future needs.

Asking, I was informed about BWA-SW.

My questions are:
-Is it the perfect program for my needs?
-In the indexing step (to create an index with my database), has the input database to be pre-aligned or the algorithm aligns it while indexing?


Thanks a lot once again.

[TabeaK]

I am not sure I understand you. So you do not have a reference sequence?

That would mean you have to assemble one first. Which means you are looking for an assembly tool; not an alignment tool.

[miguelangel]

Maybe it is a problem of words:

What I want to do is the following:

Seq1: AAAAAAGGGGGCCCCC
Seq2: AAAAAACCCCCTTTTT

---> After processing:

Seq1: A A A A A G G G G G C C C C C - - - - -
Seq2: A A A A A - - - - - C C C C C T T T T T

And what I need, first, is to assembly/align my database, so, in this way, have it as a reference for comparing future sequences, and have information about where (position respecting the database sequences) my sequences start, length of them...

I do not know if I can do it with this program.

Thanks

[TabeaK]

So; you have a lot of reads; but no reference genome? Sounds like classical assembly to me.

What organism are you working on?

[miguelangel]

I work with fungal ITS sequences, but I have a lot of reads (+/- 450pb long) of the same region, ITS-1, not correlative short sequences.

[xied75]

Sounds still like scaffolding with contigs, that's not for bwa. Although once you made this "reference", you can use bwa to align your future reads.