Software for multiple sequence alignment?

Question

[Ankit]

Hi all,

I have a fasta file for my read sequences. The reads are about 250 bp .

I am looking for a software which can align it to reference fasta (about 250 bp ) and give me the output to export.

The software should be capable of showing the indels or any missing nucleotides (let's say by dash) so that alignment remain intact. Something like this

What I next want to do is to convert this information to a matrix and quantity nucleotides coverage across each position.

If you have better suggestion for software which can do this in one step then please let me know.

I would appreciate any help.

Thank you

[WouterDeCoster]

Alignment of your sequences to the reference fasta is not the same as an MSA, as every read will be aligned to the reference 'pairwise', and there won't be any dash signs in your reference genome, just indels in your reads.

[Ankit]

Hi..

Thanks for your response.

So can you suggest a software which do the same?

[WouterDeCoster]

Then you will first have to make sure you know what you want.

[Ankit]

I want to align my reads (amplicons) to reference and obtain a file which contain alignment of bases and in case if indels are present then shows something there (eg. a special characters or "-").

I appreciate your help.