ekidna
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tseemann
Assembly based core genome SNP alignments for bacteria
Hi - really liking the tool! One suggested improvement would be to have an option to control which of the sequences gets set as your reference rather than defaulting to...
I specified 32 CPUs with `-j 32` but it looks like `any2fasta` calls were done sequentially. Would you consider parallelizing that step or making an option to skip it? For...
Hi! Long time fan of your work here! I have about 16 mitochondrial genome that I needed to find variants with, so I have been trying to use ekidna for...
The dependencies paftools and k8 can have the names paftools.js and k8-linux or k8-Darwin (macOSX) when downloaded. Unless these files are renamed to paftools and k8 then ekidna can't find...
Not clear if this is intentional but if running ekidna without the -k option the .vcf file is removed from the output. In the readme it seems to indicate that...
.. are not mentioned in the readme: * skesa * iqtree also a `paftools` binary is required but it seems the standard name is `paftools.js` Cheers! Rayan
We currently use the unaligned regions and set them to gaps in the aligement (no coverage). But the aligned regions could have small INS and DEL in them. Those DEL...
Currently the `ekidna.vcf` is made by merging all the variant VCF files. But these are ignorant of unaligned regions. Need to somehow put `.` in the positions for samples with...
Need to map sample names to input files somehow. Could use filename, but if it is just `SAMPLE/contigs.fa` will need folder name too maybe accept `-i sample_list.tab` which has `...