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tseemann
:scissors: :zap: Rapid haploid variant calling and core genome alignment
Hello, I am super new to the world of code/script etc. I am doing Covid-19 phylogenetic work. I used snippy-multi to generate indel profile before confirming using IGV and editing...
I've run it on Galaxy server using Minumum proportion for variant evidence with 0.9 or with 0.05 and as expected I got more snps using 0.05. However, after installation of...
dear all, Im having problems to run snippy 4.6.0 When I --check dependencies, I receive the following message: [11:09:57] This is snippy 4.6.0 [11:09:57] Written by Torsten Seemann [11:09:57] Obtained...
I have some problems. When using snippy, gbk file and fasta file, are downloaded from NCBI. The code is as follows: snippy --outdir test1 --ref test.gbk --ctgs test.fa [14:47:23] This...
Hi, I am trying to install snippy through conda but it just gets stuck at solving environment. I wonder if there are any suggestions to get it installed.
Dear tseemann, I m using snippy multi but samples are failing on RG tag. Can you please help me with this error. I have installed snippy using mamba. I think...
Hello Tseemann, I ran the script "snippy-core --prefix TB0065_S16_L001 TB0207_S6_L001" and I got the following error. Can you help me? This is snippy-core 4.5.0 Obtained from http://github.com/tseemann/snippy Enabling bundled tools....
Hi Dr. Torsten Seemann, Thank you for developing Snippy. I am using it to generate the snp results and alignment for 65 Mtb strain paired fastq SRR data. I need...
Hi there, When I ran snippy-core. Snippy includes reference in the alignment file, but I don't want the reference showed in the final tree. Can I just remove the ref...
Hi， I'm new to this and I want to construct a recombination free core SNP phylogenetic tree using snippy and gubbins. I'm confused because core.aln is a core SNP alignment...