Mapping ~100-300bp Sequences to Metagenome-Assembled Genomes

Question

[chemokine-1]

Hi everyone,

I'm looking for recommendations on tools and techniques for mapping short sequences to MAGs generated from a MEGAHIT assembly. Any suggestions on effective alignment tools or tips for managing large MAG datasets would be greatly appreciated.

Thanks!

Answer 1

[Mensur Dlakic]

While I use Bowtie2, there is not a strong argument for it versus other genome aligners. I guess it is because I found a pipeline back in the day based on Bowtie2 that did the job, and had no reason to switch.

You probably don't need splice-aware aligners, which gives you more options. The following paper might help:

https://academic.oup.com/bioinformatics/article/28/24/3169/245777

Even though some more recent aligners are missing in that paper (minimap2, salmon and kallisto come to mind), it should give you a good idea about available options.

Answer 2

[ALchEmiXt]

+1 for bowtie2. Also because it just does the job. If large indexes become a memory problem or if you do not want to use a local-aligner but a global-aligner, consider BBMAP.

[GenoMax]

+1 for BBMap. It should be able to do everything bowtie2 can and more. You can do local and global alignments.