snippy
snippy copied to clipboard
tseemann
:scissors: :zap: Rapid haploid variant calling and core genome alignment
Dear @tseemann, I'm running an SNP phylogeny as you suggested here: https://github.com/tseemann/snippy My problem is that if I compare the nwk tree generated by gubbins and that from IQ-tree I...
This might be a duplicate of #111 but I don't think that it was fixed -- I'm not seeing any rRNA variants in my snps.tab I've tried using the original...
Hi! I have a question regarding how to treat the snippy-core results to feed them into IQTree afterwards. So right now, I have the core.full.aln file, should I first go...
Hello, I have some questions about the input file of snippy. Can snippy mix the draft genome and the fully assembled genome from Genebank as input files? I tried to...
I have installed snippy in mac OX intel 64 using brew. No issues checking dependencies, except that the bcftools version required was 1.7 and the one installed was 1.16. I...
Dear all, I run the code "snippy --outdir 'SJ_2016_1531' --R1 '/home/ND140/lm/cgMLST_test/SJ_2016_1531_R1.fastq.gz' --R2 '/home/ND140/lm/cgMLST_test/SJ_2016_1531_R2.fastq.gz' --ref /home/edwin/template/bwa/tb_h37rv.fasta --cpus 16", it showed "Error running command, check SJ_2016_1531/snps.log". ### samtools faidx reference/ref.fa ### bwa...
Hi, I'm using snippy-multi to obtain core-genome alignment and core SNPs among about 500 bacteria strains. I tried to run twice independently using same dataset and same parameters, but the...
Solution: The running memory is greater than 8G 电脑内存大于8G
This is my command: snippy --outdir snps_output_rep4 --ref GCA_018093105.1_ASM1809310v1_genomic.fna --ctgs S.aureus_bat3_r3..contigs.fasta I am getting error while running samtools markdup I am using contigs and ref genome in fasta format. PLease...
I had the error with libtabixpp0, when I fixed this I seemed to loose bcftools. I have forced reinstall (bcftools and snippy) multiple times including downgrading but I keep coming...
