Enable more options to vary the BowTie2 alignment parameters during host removal and alignment

[alexhbnr]

Description of feature

Ancient DNA has the characteristic substitution pattern compared to the reference genomes at the terminal bases of reads, i.e. increase of C>T substitution at the 5' end and G>A substitutions at the 3' end of reads. These substitutions have a direct impact on the success of aligning sequencing data against a reference genome or the de novo assembled contigs. During the alignment, BowTie2 tries to infer the location of a read using seeds. By default, no mismatches in the seeds are allowed (-N 0) and therefore some reads might not be correctly aligned to the reference in case there is a mismatch in the seed caused by these aDNA-specific substitutions.

By allowing to customise the BowTie2 alignment parameters more freely, one could set the option -N to 1 for ancient DNA to avoid having a low number of aligned reads either to the host genome or to the assembled contigs.

[jfy133]

Looking through the documentation, actually this is already possible via:

https://nf-co.re/mag/2.2.1/parameters#bowtie2_mode

The mode is a bit misleading as it suggests it corresponds to fixed 'presests' in Bowtie2, but in fact it's a string that you can put whatever you want.

I guess then the question is should I fix this to the presets and or make -N an explicit option, or just leave what already exists? What do you think @alexhbnr ?

[alexhbnr]

No, I was also under the impression that it was specific to select the BowTie2 prefix. If we can also append -N 1 for ancient samples, there is no need to add an explicit option, I think.

[jfy133]

OK actually this only applies to aligning reads back to the assembly (this is actually what is set during the 'ancient DNA mode', however it's not used in the PHIX/Host removal, should I apply it to these others too?

Should these be independant (I guess you don't need a mismatch for phiX removal...?), or just blanket is OK? And should I associate this with the 'ancient DNA mode' as with the assembly alignment?

        ext.args = params.bowtie2_mode ? params.bowtie2_mode : params.ancient_dna ? '--very-sensitive -N 1' : ''

which is currently like this

[alexhbnr]

You are right, for phiX removal we wouldn't need this adaptation. For the host removal DNA, it is a matter of preference. In most cases we have only a low proportion of host DNA that has to be removed. In this case, it doesn't really matter whether we enable -N 1. So let's keep it like it currently is and just allow to enable -N 1 for the alignment back to the assembled contigs.

[jfy133]

Thanks!