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snp-dists833.10.332.833.133.7 psdm1617.60.217.417.518.0 snp-dists1620.70.220.420.721.1 Contributing Contributions are always welcome. For changes to be accepted, they must pass the CI and coverage checks. These include: Code is formatted (cargo fmt). ...
For larger alignments such as the Maela pneumococcal data set (3e5 x 3e3) the c++ version is approximately an order of magnitude faster than approaches based on pairwise comparison of every site such as snp-dists from which the skeleton code for the c++ version was taken....
snp-dists snp-sites snpeff 5.1 5.2a Dockerfile README.md test_snpeff_snpsift.sh snvphyl-tools spades sratoolkit srst2 staramr stxtyper sylph tbprofiler tests tiptoft tostadas training treemmer trimmomatic trycycler unicycler vadr verkko vibrant vigor4 viridian virsorter2 virulencefinder wtdb...
snp-dists snp-sites snpeff 5.1 5.2a Dockerfile README.md test_snpeff_snpsift.sh snvphyl-tools spades sratoolkit srst2 staramr sylph tbprofiler tests tiptoft tostadas treemmer trimmomatic trycycler unicycler vadr verkko vibrant vigor4 virsorter2 virulencefinder wtdbg2 .gitattributes .gitignore .g...
#!/bin/bash # tests for QuickSNP 1.0.1 #Exit immediately if a command exits with a non-zero status set -e #Running QuickSNP QuickSNP.py --dm ./test_data/test_snpdist.tsv --outtree ./test_data/test_1.nwk # Checking if the outputs match if cmp --silent -- ./test_data/test_...
Usage: quanttb makesnpdb [options] <-g> Required arguments: -g [DBFILES ...] Files you want to use to make the reference database, Can be either .fa, .fna, .fasta, .snps .vcf(.gz), or .samp Optional arguments: -reducedist When making database, what is the minimum distance ...
skani skesa smalt snippy snp-dists snp-sites snpeff 5.1 5.2a Dockerfile README.md test_snpeff_snpsift.sh snvphyl-tools spades sratoolkit srst2 staramr sylph tbprofiler tests tiptoft tostadas treemmer trimmomatic trycycler unicycler vadr vibrant vigor4 virsorter2 virulencefinder wtdbg2 .gi...
#!/bin/bash # tests for QuickSNP 1.0.1 #Exit immediately if a command exits with a non-zero status set -e #Running QuickSNP QuickSNP.py --dm ./test_data/test_snpdist.tsv --outtree ./test_data/test_1.nwk # Checking if the outputs match if cmp --silent -- ./test_data/test_...
#!/bin/bash # tests for QuickSNP 1.0.1 #Exit immediately if a command exits with a non-zero status set -e #Running QuickSNP QuickSNP.py --dm ./test_data/test_snpdist.tsv --outtree ./test_data/test_1.nwk # Checking if the outputs match if cmp --silent -- ./test_data/test_...