snippy
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tseemann
:scissors: :zap: Rapid haploid variant calling and core genome alignment
After running snippy on multiple isolates, with command snippy-multi , i have run recombination detection tool as given: %run_gubbins.py -p gubbins clean.full.aln % snp-sites -c gubbins.filtered_polymorphic_sites.fasta > clean.core.aln % FastTree...
I'm calling variants from 10 samples using one reference fasta for all. The samples are from the same strain. One sample is WT and the others were under different stress...
Hello, I have already used snippy and snippy-multi in my previous work. I have recently installed snippy into a new PC but I think snippy-multi is not exported. Whenever I...
Hi Torsten Seemann, Thanks a lot for developing and maintaining snippy! I'm using your tool to study deletions. While investigating the output for deletions I realized that I ether don't...
Running one sample at a time works OK, can't create runme.sh $snippy-multi input.tab --report --html --cpus 7 --ref /home/shawndy/Biomatics/snippy/C01_assembly.fasta > runme.sh causes: ERROR: [C01_/home/shawndy/Biomatics/snippy/C01/Sample1.R1.fastq_/home/shawndy/Biomatics/snippy/C01/Sample1.R2.fastq] missing read/contig data: C01 /home/shawndy/Biomatics/snippy/C01/Sample1.R1.fastq /home/shawndy/Biomatics/snippy/C01/Sample1.R2.fastq...
I was using Snippy and I recommend the use of this software. Great Job! When I ran it with a reference in gbk file format Snippy split it into Fasta+GTF...
Hello, @tseemann my friends tried to make a loop on output that we got from running bbduk on snippy code example provided by you but it won't work the output...
I have run 25 samples on snippy-multi and individually all runs seem ok but in core.txt only shows 1 snp for the last file.
