Consider adding nonpariel - 'preseq for metagenomic taxonomic profiling'

[jfy133]

Is your feature request related to a problem? Please describe. Given the rising increase in microbiome studies, it might be good to include an additional QC step for deeper sequencing calculations for metagenomes.

Describe the solution you'd like This can be done with nonpariel https://academic.oup.com/bioinformatics/article/30/5/629/246142 http://enve-omics.ce.gatech.edu/nonpareil/index

Advantages:

• It's already in conda
• Sort of like Preseq but doesn't require reference, runs just on FASTQ files

Describe alternatives you've considered

Disadvantage:

• we already have Preseq so maybe sort of giving reundency (but see above)

It might not be so relevent given EAGER is meant to be genome reconstruction, but as we have MALT for first step as pathogen screening, it could be useful?

It would be good to get other people's opinions on this.

[jfy133]

Doesn't support gzipped reads, so this will result in large HDD usage and I would rather not on already such a large pipeline...