Guidance regarding Snipe output

[NienkeMekkes]

Dear authors,

Thank you for creating this tool. I was testing this tool in the following way: I created a metagenomic dataset consisting of 13 different salmonella strains with an abundance of 0.001 each, and one E.coli strain at 0.987. All strain reference genomes were downloaded from NCBI. When profiling this dataset with Kraken2 and bracken, I find some false positive species entering the data, and some deviations in abundance, however, the output is pretty good.

For snipe, I added the accession numbers and strain designation to dict target and dict template when they were not present for the REC module. I used the default clostridium genome in filter.fna and I added the paths to the reference genomes as targets for the MAP module.

I get the following output. I added the columns genome and truth, for the used genome and known input abundance that I simulated. The initial best hit output is copied from the output of the ID module, which is pretty close to the truth. However, after running REC, I do not see an improved in the output, or I am misunderstanding the output or way to run Snipe. Could you provide guidance on how to use Snipe to reduce false positive hits? Or, should I change how I run Snipe, and add more target or filter genomes? Here I only used the genomes I know to be in my simulated sample as targets.

Genome	truth	Initial Best Hit	Rectified Final Guess	Final Guess	Rectified Probability	SSR Aligned Reads	Rectified Abundance	Initial Abundance	Final Best Hit	Final Best Hit Read Numbers
E.coli strain A	0.987	0.98406	0.00000	0.98717	0.00000	0.00000	0.00000	0.98718	0.98718	6581197.00000
Salmonella strain 1	0.001	0.00133	0.00000	0.00671	0.00000	0.00000	0.00000	0.00723	0.00723	48178.00000
Salmonella strain 2	0.001	0.00125	0.00000	0.00166	0.00000	0.00000	0.00000	0.00175	0.00175	11669.00000
Salmonella strain 3	0.001	0.00124	0.00004	0.00004	1.00000	6529.00000	0.00004	0.00004	0.00004	261.00000
Salmonella strain 4	0.001	0.00123	0.00000	0.00027	0.00000	0.00000	0.00000	0.00018	0.00018	1201.00000
Salmonella strain 5	0.001	0.00123	0.00000	0.00018	0.00000	0.00000	0.00000	0.00015	0.00015	999.00000
Salmonella strain 6	0.001	0.00120	0.00221	0.00221	1.00000	6529.00000	0.00180	0.00180	0.00180	12030.00000
Salmonella strain 7	0.001	0.00120	0.00001	0.00001	1.00000	6529.00000	0.00001	0.00001	0.00001	48.00000
Salmonella strain 8	0.001	0.00117	0.00000	0.00001	0.00000	0.00000	0.00000	0.00001	0.00001	82.00000
Salmonella strain 9	0.001	0.00117	0.00113	0.00113	1.00000	6529.00000	0.00115	0.00115	0.00115	7664.00000
Salmonella strain 10	0.001	0.00117	0.00042	0.00042	1.00000	6529.00000	0.00032	0.00032	0.00032	2104.00000
Salmonella strain 11	0.001	0.00116	0.00000	0.00000	1.00000	6529.00000	0.00000	0.00000	0.00000	24.00000
Salmonella strain 12	0.001	0.00115	0.00000	0.00002	0.00000	0.00000	0.00000	0.00002	0.00002	139.00000