snippy
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tseemann
:scissors: :zap: Rapid haploid variant calling and core genome alignment
Hello, I am having issues. And below is the log file. Thanks ### samtools faidx reference/ref.fa dyld: Library not loaded: @rpath/libcrypto.1.0.0.dylib Referenced from: /Users/User/miniconda3/bin/samtools Reason: image not found
Hi Torst This is a little script that can be used to aggregate more than 1 snps.tab files from multiple Snippy runs (assuming same reference) into a single tab file...
I trimmed the reads using trimmomatic first and tried to run Snippy. However, I am surprised to find out the snippy does not take both paired-end reads and unpaired ones...
So this one is a bit of a weird and long one. I am using snippy v. 4.6.0 installed through conda in a centos based system. The datasets I am...
Hi @tseemann I use my previous command that worked well with my previous ubuntu and conda environment. The command is snippy-core --ref K96243.gb 10-* When use this command with snippy...
I ran snippy and found that one of the samples did not call the target SNP. Upon performing samtools mpileup, I found that the missing SNP had the following flag:...
I've been looking for a SNP-caller that does not depend on a reference genome. How hard would it be make snippy work on the core genome of a set of...
