Aligning Neanderthal vs human genome using Bowtie

Question

[skr3178]

Hi, I am new to Bioinformatics in general. I already have found resources for already aligned Neanderthal and Denisova genome here: http://cdna.eva.mpg.de/neandertal/altai/AltaiNeandertal/bam/

I am interested in Aligning Neanderthal vs human genome using Bowtie2. I am wondering if that is already done before (if so can someone point out the link). Also wanted to learn what kind of computational resources are needed for such alignments (in terms of RAM, CPU)? Those requirements I guess can be drastically reduced by using one chromosome at a time or a sections. Thanks, Skr3178

Answer 1

[Istvan Albert]

the alignments you speak of are short-read, where measurements from neanderthal DNA were aligned against the human genome.

There is no separate Neandertal genome assembled that I know of. Hence you couldn't align the two.

If even if there were such genomes you could not align them via bowtie anways, since that tool was designed for short read alignments.