-
Hi,
Thanks for such useful tool!
I've been following your Example 03: Metagenomic application - Metagenomic analysis of the Ethiopian cohort, but I got stuck in the least section of drawing heatmaps…
-
Hi, I ran pggb to build pangenomes for 10 bacterial genomes (Ecoli). The command is `pggb -i merged.fa.gz -o 10n95p -t 20 -p 95 -n 10 -S -m` and it can work well. But i have some confused with the par…
zwh82 updated
11 months ago
-
Hi, I have a question regarding the --enable-score-calibration flag. I understand that it considers the composition of the sample to output a 'real' probability, e.g. plasmid score of 0.4 would mean t…
-
Hi,
Is there a way of getting BandageNG to output connected components as separate assembly graphs? I work with metagenomes and it would be extremely useful to be able to do this and then work on t…
-
here are some thoughts I wrote up for a collaborator, thought I'd share broadly -
The default FracMinHash approach will yield overlap estimates when applied to two metagenomes. In technical terms t…
-
Hi,
Thank you very much for creating a good tool Ganon, I am using Ganon for taxonomic profiling but my target is not only bacteria and viruses, but also to identify species belonging to algae, fungi…
-
Thank you for developing such an excellent tool. Since NextPolish was not tested in metagenomic data which has strain-level polymorphism(similar to haplotypes), I wondered if there were any problems w…
-
E.g.
```
/ NCBITaxon:1 ! root
is_a NCBITaxon:12908 ! unclassified sequences
is_a NCBITaxon:408169 ! metagenomes ***
is_a NCBITaxon:1235509 ! synthetic metagenome
is_a NCBITaxon:256318 ! …
-
Looks like a [potential complement](https://www.nature.com/articles/sdata2018176) to MGnify data:
> dataset comprising over 5 terabases of metagenomic data from 610 samples spanning diverse region…
-
Since this is designed for a meta-NGS data set - and Bowtie2 is not (he says so in his manual).
- BT2 is a *greedy* matcher = very low %ID matches will still be reported, it was designed for a si…