Generate annotated SNP tables and phylogenetic trees.
235
This image implements:
and the Dockerfiles can be found on github.
Get test data:
mkdir -p data
cd data
# Download test data
git clone https://github.com/USDA-VS/vsnp3_test_dataset.git
Add reference to path:
cd vsnp3_test_dataset/vsnp_dependencies
vsnp3_path_adder.py -d `pwd`
Run Step 1:
cd ../AF2122_test_files/step1
vsnp3_step1.py -r1 *_R1*.fastq.gz -r2 *_R2*.fastq.gz -t Mycobacterium_AF2122
sha256sum alignment_NC_002945v4/*_zc.vcf > ../../../step1.checksum
Run Step 2:
cd ../step2
vsnp3_step2.py -wd . -a -t Mycobacterium_AF2122
sha256sum Mbovis-All/*.fasta > ../../../step2.checksum
Content type
Image
Digest
sha256:17d3bd634…
Size
3 GB
Last updated
about 4 years ago
docker pull gregorysprenger/vsnp3:v3.09