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tseemann
:scissors: :zap: Rapid haploid variant calling and core genome alignment
Output ---------- This wouldn't affect core genome alignment or anything case-insensitive downstream from running `snippy-core`, just want to have correct count of variant sites from the `.full.aln` in the `PREFIX.txt`...
Hi, Does anyone tell me how the evidence column is calculated in the SNIPPY tool? Similarly, there is the term stop gained and conservative inframe deletion and insertion. Thank you!
Hi! I have a big question. When running snippy-core are the low quality SNPs called with snippy filtered out? I'm running snippy+snippy-core on 386 E. coli isolates and I'm getting...
Hi everyone, I am facing an issue while using snippy-multi. It returns 0 SNPs. I have tried one of my genome individually with the snippy command and it returns 22...
Hi Snippy moderators Could you help me review this ? I keep getting Bad ID error NexGen:~$ snippy-multi input2.tab --ref home/medp8144/test/1.fasta --cpus 2 > runme.sh Reading: input2.tab ERROR: Bad ID:...
When I typed "mamba install snippy=4.6.0" and got it successfully I used this software to run my data.But I met an question about this vcfuniq: symbol lookup error: lib/libvcflib.so.1: undefined...
Hi everyone, I am facing an issue while using snippy-multi. It returns 0 SNPs. I have tried one of my genome individually with the snippy command and it returns 22...
hello,i have a question i cannot deal. here is my code: snippy-multi snp.txt --ref sequence.gb --cpus 40 > sy.sh sh sy.sh output: [11:08:18] Using read file: /home/data/zzz/China-pig-309/GCA_003310565.1_ASM331056v1_genomic.fasta [11:08:18] Output folder...
I use snippy 4.6.0 to calling my bacteria snp,but there are no result ,I wonder what to do next ,thanks. snippy --outdir 135080RSH2439 --ref 175001_wt/175001R1qc_shovill.fasta --ctgs 135080RSH2439.fasta [21:19:19] This is...