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Hi,
Some of the systems I want to find can be differentiated from systems I'm uninterested in because they have two genes nearby that hit the same HMM. How might I go about defining this in the XM…
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hi,
thank you for this amazing tool. what is the minimum overlap 2 sequences can have, so that minigraph will construct a node shared by the 2 underlying genomes?
i am asking bc/ when i construct a …
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Hello John,
thank you for a very interesting tool. I'm trying to fit a model for about ~ 3000 genomes of specific Salmonella serovar (Enteritidis). Problem is, it seems, that its pangenome is not …
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Dear PANAROO team,
I started to use your tool (v1.1.2 installed through conda) few days ago and I think I found a bug (or something I do not understand :) ).
For some groups, I cannot find a re…
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## Reference construction
Currently the skylab repository creates a number of references that are used by smart-seq 2, Cellranger, and Optimus. These include:
- hisat2
- rsem
- star
- cellra…
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Hi John,
As discussed, I've been running the --lineage-clustering option.
`poppunk --lineage-clustering --ref-db strain_db --external-clustering Global_TPA_SS14-mapped_2020-06-09.noINDELS.fix-m…
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Hello,
What does it mean when I get a NOTE message saying "sample required densification"?
I get this note when I try building an _E. coli_ database, setting the sketch size to 1,000,000 (--min-…
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Hello,
I installed panaroo through conda and I ran it twice for pan and core alignemnts but the pan genome does not produce any different output except the lack of core gene alignment file and the…
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Hello,
I am using sourmash to de-duplicate metagenome-assembled genomes. I tried the tutorial at http://sourmash.readthedocs.io/en/latest/tutorials.html#compare-many-signatures-and-build-a-tree and…
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While trying to calculate a comparison to the sketchlib output (which worked fine with the same input seconds previously, in easy-run mode), I encountered this error - seems like there might be an iss…