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tseemann
:scissors: :zap: Rapid haploid variant calling and core genome alignment
Hi @tseemann When I update my snippy to 4.6.0, I got 0 varaint after runing. snps.csv contain nothing. Please see my snps.log below Your response is greatly apriciate ! ###...
I'm trying to run snippy-multi for a few assembled genomes. I've generated a tab file (input.tab) as follows: isolate12 /msa/12_PROKKA_06152021.fna isolate2 /msa/2_PROKKA_06162021.fna isolate25 /msa/25_PROKKA_06162021.fna isolate87 /msa/87_PROKKA_06162021.fna isolate3 /msa/3_PROKKA_06152021.fna isolate32 /msa/32_PROKKA_06162021.fna...
Dear Torsten, we use snippy in order to align the reads to a reference and to obtain the annotation of the variants. Unfortunately in the results that we obtain we...
Hi, I successfully ran snippy and now want to do some core phylogeny for my SNPs. I created the input.tab file using fastq files and fasta files(some of my samples...
Hi, just a quick question. I used snippy-multi to generate my script but because I only supplied the one fastq, it automatically added --se . In fact, these are paired...
Dear everyone, I used snippy to check SNP compared to reference H, pylori 26695. However, I got this error. Does anyone get same problem with me? Thank you ### echo...
Objective: I am trying to use Snippy to generate a .vcf SNP discovery file using (1) .fasta and (2) .fastq as input files. Problem: After 5 days (8 cpus), there...
Hi, I am getting strange results from snippy-core: I ran contigs from 100 isolates using snippy-multi (therefore all against the same reference) and then generated a distance matrix from the...
Hello @tseemann and all users, I am running snippy with basic configurations and keep getting the following error (even when change the reference from FASTA to GenBank): [variant_manip.cpp:75 is_ref_consistent] Variant...
Hi, I'm trying to run snippy but I get the error: "Can not read sequence file" and I don't know how to solve it. My input files are reads in...
