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I ran this code:
./genome-wide_localLD_scan.r -a core_alignment.fasta -o '/home/ubuntu/genomescans/output' --LD.metric=Fisher -f '/home/ubuntu/genomescans/pangenome_alignment.gff' -T 4 -K 4900
An…
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Hi Kraken2 developers, thanks for developing this amazing tool.
I am working with a bacterial species with **high degree of intra-species genomic variations** (SNPs spread across the core genome, a…
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Hello,
I have tried the co-assembly method.
I was looking into the classification details on the files 10.* and 06.*, I noticed that I got the species but not the strain information in my classifi…
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I tried to run Roary on 7 different bacterial strains (draft Illumina assemblies, annotated with Prokka). I'm not entirely sure how related the strains are, maybe we have more diversity in there than …
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plot_matrix_heatmap.sh -i pangenome_matrix_t0.tab -o pdf -N -H 8 -W 14 -m 28 -v 28 -t "pangenome" -k "genes per cluster"
# Plotting file pangenome_matrix_t0_heatmap.pdf
Error: There are less than …
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Very quick question about how to get the actual DNA sequences from the inferred accessory genome. I would like to extract these sequences to do some blastn analysis and also for metagenomic purposes. …
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I have created/read the Issues page (issue (#267)) where it is said that core genome alignment from Roary is not suitable for Gubbins to detect recombination. But from time to time I find publications…
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Hi Elaina,
I'm wondering if you would please explain the final output to me. Particularly the BinSanity-Final-Bins directory.
I'm using Binsanity to try to recover MAGs from metagenomic samples an…
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The manual says:
```
First of all we construct a FASTA file with the binary presence and absence of genes, where 'A' means a gene is present and 'C' means it is absent. Only the first 4000 genes in t…
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The SWG today (2020-05-27) discussed whether the development of **OGC API - Common - Part 2: Collections** might have implications for **OGC API - Coverages**. The SWG agreed to revise the document, i…