Query on bowtie2
Instead of a complete reference genome, I have contigs of the reference to which I want to align my Illumina reads. Can bowtie2 be used for this purpose? I am not sure how it deals with reads which fall at the contig breakpoints, does it still align them?
Thanks!
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You can use any sequence as reference including contigs when you create
bowtie2indexes. If a read aligns to two contigs you should be able to see if it is aligning at ends of contigs.Thanks! So I can check this with IGV?
In theory. You may need to find alignments that explicitly have alignments to two contigs and see what those look like in IGV. Here is an overview paper for variant review using IGV.
Thanks a lot! This really helps