parsnp
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marbl
Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includ...
Hello. I am currently analyzing the SNVs for 400+ fungal genomes for pangenomic analysis. I was just wondering if the indel information for the multiple sequence alignment is stored in...
Hello, I'd like to have a file where I can identify the snps with the gene and I tried the command: `harvesttools -i parsnp.ggr -M msa_lcb.aln ` and it stucked...
Sometimes I have just 1 new isolate I'd like to compare against a larger parsnp run of a couple thousand genomes. Re-running from scratch can take 2+ days to analyze....
Hello. Currently running mac and downloaded harvesttools using conda. When I run normal parsnp command, I get the following error: base) > ~ % parsnp -g ~/GCF_PAO1_000006765.1_ASM676v1_genomic.gbff -d ~/WR_fna -p...
We have 41 complete, closed, Salmonella sequences (40 unique). For a reference to get annotations, we exported one (1956) as both a genbank file, and a fasta file. Looking at...
We are having a problem that ParSNP returns different numbers of SNPs when run on the same input but on different computers. [Here](https://github.com/SarahNadeau/bioinf-containers/blob/master/parsnp/tests/scripts/run_real_data.sh) is the script we're running - it...
Hi, I'm currently trying to use parsnp v1.5.4 on a slurm cluster (with raxml v8.2.12, PhiPack/1.0, harvest-tools/1.3, FastTree/2.1.11) and I keep getting an error when trying to run parsnp on...
Hi, I'm currently using parsnp v1.5.3 on a slurm cluster (with raxml v8.2.12) and I keep getting an error when trying to run parsnp on ~13,000 bacterial genomes. Any idea...
Todd, If I create a folder called 'fasta' with 20 small identical fasta files and run "parsnp -r '!' -d fasta" and run it, often my resulting tree only has...
Dear developers, I'm trying to use your tools for core SNP analysis. I use a native Ubuntu 20.04, the tutorial works fine but when I run my samples I have...
