snippy
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tseemann
:scissors: :zap: Rapid haploid variant calling and core genome alignment
I tried to run snippy with the following genbank file: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/008/632/635/GCF_008632635.1_ASM863263v1/GCF_008632635.1_ASM863263v1_genomic.gbff.gz However, the pipeline failed for me when snpEff started. My snpEff version is SnpEff 5.2a (build 2023-10-24 14:24) The...
### samtools index snps.bam ### fasta_generate_regions.py reference/ref.fa.fai 637096 > reference/ref.txt ### freebayes-parallel reference/ref.txt 4 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60...
Hi, I have this error that seemed to be coming from freebayes, I have googled but still have no idea of how to solve it. ### freebayes-parallel reference/ref.txt 8 -p...
Hello, I am trying to use snippy 4.6.0 via miniconda3 on Linux and the output given indicates my samples have 0 variants compared to the reference genome. The created snps.csv...
Thanks for create snippy. It is very useful tools, it help me very much when working. During working, I must work with one reference (human genome) many times. Can i...
Hi everyone! Snippy generates two different sized alignment files core.aln and core.full.aln. which alignment file will be used to create SNP matrix to study clonal samples? Whether Core.full.aln contains core...
Hello everyone, I am running snippy typing: snippy --cpus 5 --outdir var --ref sequence.gb --pe1 R1_trimmed.fastq.gz --pe2 R2_trimmed.fastq.gz Receiving this error: Error running command, check var/snps.log When I check this...
I suspect there might be something wrong with my installation. Do you have a read set that I can use to test the installation?
Hi tseemann, I am use snippy 4.6.0, and I am wondering why samtools excluded most of the reads. In the end, I got no variant (I am expecting variant), and...
Hi there! I would love to use snippy for "mixed" datasets with multiple bacterial genomes in. At the moment I am getting mixed mapping to the rRNA operons. Is there...
