ummidock/seqsero2
SeqSero2 is a pipeline for Salmonella serotype determination from raw reads or genome assemblies
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ummidock/seqsero2 repository overview
docker-seqsero2
Docker image with SeqSero2 software (GitHub page).
SeqSero2
"SeqSero2 is a pipeline for Salmonella serotype determination from raw sequencing reads or genome assemblies.". From here.
Usage
You can download and run this image using the following commands:
# Get Docker image
docker pull ummidock/seqsero2:alpha-test-1
# Run SeqSero2 in K-mer mode using reads
docker run --rm -u $(id -u):$(id -g) -it -v /local/folder/data:/data/ ummidock/seqsero2:alpha-test-1 SeqSero2_package.py -p 1 -t 2 -i /data/sample_1.fastq.gz /data/sample_2.fastq.gz -d /data/out_kmer_reads
More examples on how to use SeqSero2 (outside a Docker container context) can be found in SeqSero2 GitHub page
Image Content
This Docker image contains:
- SRA Toolkit v2.9.1
- SalmID v0.11
- Biopython v1.71
- BWA v0.7.17-r1188
- Samtools v1.7
- Blast v2.6.0+
- SPAdes v3.12.0
- Bedtools v2.27.1
Citation
If you use SeqSero2 in your research, please cite:
Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X. Salmonella serotype determination utilizing high-throughput genome sequencing data. J Clin Microbiol. 2015 May;53(5):1685-92. doi: 10.1128/JCM.00323-15. Epub 2015 Mar 11. PubMed PMID: 25762776; PubMed Central PMCID: PMC4400759.
If you use SeqSero2 using this Docker image, please add:
SeqSero2 was run using the Docker image “ummidock/seqsero2:alpha-test-1” (https://hub.docker.com/r/ummidock/seqsero2/)
Tag summary
Content type
Image
Digest
Size
1.8 GB
Last updated
over 8 years ago
docker pull ummidock/seqsero2:alpha-test-1