Sam Chorlton

Single-end metagenomic data

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### Is your feature request related to a problem? Please describe. For generic questions use Q&A section in the Discussions forum above. Sorry if I missed this in open issues...

Make hardier

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I suppose it's a bit hard to see the diffs as Github doesn't account for moved files, but in summary: 1. Set `-euo pipefail` to make it fail when a...

Docker in docker permission issue

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When using the girder_worker docker image, unable to run docker from within the worker container due to permission issue. Specifically the docker group does not appear to be created and...

Merge simple edges in the assembly graph?

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Hi @voutcn and @aquaskyline, I ran megahit 1.2.9 and got the following graph with `megahit_toolkit contig2fastg 141 final.contigs.fa`:  Note the contig subgraphs I have highlighted in the red boxes...

Hi @Vini2 , Thanks for the great tool. More a conceptual question, your manuscripts all discuss binning of contigs, which seems to make sense to me (especially for paired-end Illumina...

Thanks for the great software! I'm wondering if it makes sense to weigh binning results with a confidence metric? A toy example I'm thinking of is: 3 contigs total, all...

Exception: Don't know how to handle this mutation

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Thanks for the great tool. This looks similar to https://github.com/jodyphelan/TBProfiler/issues/258 but on official latest ([1656b7fe64c5543d55cf52b55de67b2344e9564f](https://github.com/jodyphelan/tbdb/tree/1656b7fe64c5543d55cf52b55de67b2344e9564f)) tbdb. It may just be that you haven't had a chance to update tb-profiler yet...

Thanks for the great tool. I'm of the opinion that Kleborate should not use more than 1 thread unless allocated more via a command line arg as I suppose it...

Save seed index to disk

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Thanks for the great software. Is there a way to save the seed index to disk so it doesn't need to be generated each time? I see a hidden option...

Kraken2 outputs kraken reports without a "Root" line if all reads are unclassified. I have not tested the other Kraken versions. This fixes an error where the tree is uninitialized...