Competitive mapping for strain separation

[EisenRa]

In some metagenomic contexts, there can be closely related species in a sample that can make read mapping to a single reference genome difficult (e.g. cross-mapping of reads between species). In this situation, it can be useful to employ competitive mapping, whereby reference genomes from closely related species are concatenated (in a multifasta), and the reads mapped to this reference. This can allow for the mapping quality filter to filter out reads that would cross-map between species.

EAGER could allow users to select a folder, or a list of reference fastas and concatenate them into a multifasta prior to read mapping. Alternatively, the user could provide their pre-concatenated multifasta file.

Regarding the output of mapping stats, the concatenated BAM file would have to be split using bamtools prior to generating stats.

[apeltzer]

I guess this goes the same way as #5 , with the minimal adjustment of making these available as multiFastA files. I guess that should be feasible in that scope too.

[jfy133]

After doing something similar in another situation, I agree @EisenRa 's suggestion of making a multiFasta file reference file and mapping to that is probably the way forward, rather than having the multiple channel thing mentioned in #5. One might not even have to split the bamfile, (unless we have an option of spitting out a particular genome from the bam file), as most tools are human-focused that report per-chromosome statistics.

[jfy133]

This could also be of interest but outside of the metagenomics stuff, for improving non-human mappings: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07229-y

[jfy133]

Going to close in favour of #878 which is more requested and arguably more powerful.

Like above, extracting stats with e.g. bed tools (already supported) should be sufficient in many cases.