Amanda

License request

1

Hi, I work at a small biotech startup in London - is it possible to get a non-academic license to use geNomad for R&D purposes? I emailed [email protected] a while...

How does Sourmash cope with genome redundancy in GenBank reference genomes

4

Hi again! Just thinking about the RefSeq versus GenBank question for analysis of a metagenome (containment). Aware that Sourmash may struggle with similar genomes (ie strains) due to a smaller...

ANI calculation

2

Hi, Could you help me to understand how QueryContainmentAni and MatchContainmentAni are calculated? Given the use of exact kmer matches, I would assume that the ANI between a query kmer...

Application of `f_unique_to_query` and `threshold_bp`

5

Hi, I am using Sourmash to profile bacteria composition and abundance in shotgun WGS stool samples, and have two questions: Could you expand on what you mean by this statement...

Same ASV assigned to different taxonomy in two samples

1

Hi, Im looking to get consistent results per samples such that sample X in cohort A will have the same results as the same sample X in cohort B. I...

Error message: Can't find files for block a expected files such as

1

Hi, Im getting a DADA2 error message when running lotus2 (DADA2 + lambda) on some paired reads. Ive pasted some of the log output below. One thing I noticed was...

Merging results from two lotus2 runs

1

Hi, I have data from 3 projects that I would like to compare. The methods were very similar but error rate liley vary, hence I would like to run them...

Using lotus2 with input ASVs

5

Hi, I have ASVs across a set of samples- can I run these through lotus 2 lambda using the taxOnly flag? My guess is I need to create a fasta...

Hi, I'm using emapper-2.1.12 to search for kegg orthologs (KO) and link to kegg reactions. One of my query proteins has been matched to KO K22317, but has not associated...