Alignment of genomic resequenced data to reference genome

Question

[kirannbishwa01]

I am working with population specific re-sequenced genome data from A. lyrata. I need to align it to the reference genome which is already available and prepare population specific sequence. I will also do variant calling but for now alignment of fragment to reference genome is what I am interested in.

Could anyone suggest of a pipeline/apps combination that would be helpful for this purpose?

Thanks,

[Ram]

Did you look at (read Google) the tools available for short read alignment?

[TriS]

http://en.wikipedia.org/wiki/List_of_sequence_alignment_software#Short-Read_Sequence_Alignment

Answer 1

[TriS]

I like bowtie2, you can find the manual here. from the results files you can then use SAMTools BCFtools to find variants.

As a VERY general guide your steps should be:

1. Build bowtie2 index with bowtie2-build (bowtie2-build -f myFastaGenome myOutputBaseName)
2. Align with botwie2(bowtie2 -x myOutputBaseName -f myFastaFile -S mySamOutput)
3. Index reference seq with samtools(samtools faidx myFastaGenome)
4. Convert previous sam to bam (samtools -view -bS mySamOutput > myBamOutput)
5. The command line here

You need to find the A. lyrata reference genome, not sure if [this][4] helps.

Answer 2

[kirannbishwa01]

Thanks RS. I had read about this but I need something that has documentation and potentially already worked out examples to guide me through the process. Examples always help me understand the data better and helps with interpretation. I have been trying to work with BBmap but for right now I am trying to get it work first. I will see how it goes.

Thanks