Alignment to multiple reference sequences

[cbaudo]

Hello,

I'm interested in determining if plasmid sequences are in a NGS data set and I was thinking about creating a master fasta file with the sequences for each plasmid and then aligning NGS data to that master file and determining 1) if the sample has a plasmid and 2) which one(s).

My questions are 1) Does it make sense to use one fasta file containing all the plasmid sequences
>plasmid 1
ATGC
>plasmid 2
AGCT
>Plasmid 3
ATGTT

or should I have one fasta file for each plasmid?

2) What software could I use to visualize which plasmid has reads mapping to it? If multiple plasmids are mapped to, etc.?

Thank you

[GenoMax]

You can put multiple plasmids in one file (fasta identifiers would need to be unique). You can use IGV with this "custom genome" and be able to switch between the plasmids as you view.

Hopefully these plasmids don't share significant sequence homology, otherwise you are going to have trouble uniquely assigning reads to individual plasmids. You could allow them to multi-map at all possible locations.

Take a look at BBSplit to see if that may be something you want to try (to bin your reads into plasmid specific bins) before alignment.

[cbaudo]

Thanks Geno!