mapping_to_phandango
genomic sequence element (kmer) enrichment analysis
Install
- All systems
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curl cmd.cat/mapping_to_phandango.sh
- Debian
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apt-get install seer - Ubuntu
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apt-get install seer - Kali Linux
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apt-get install seer - Windows (WSL2)
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sudo apt-get updatesudo apt-get install seer - Raspbian
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apt-get install seer - Dockerfile
- dockerfile.run/mapping_to_phandango
seer
genomic sequence element (kmer) enrichment analysis
Bacterial genomes vary extensively in terms of both gene content and gene sequence - this plasticity hampers the use of traditional SNP-based methods for identifying all genetic associations with phenotypic variation. SEER provides a computationally scalable and widely applicable statistical method for the identification of sequence elements that are significantly enriched in a phenotype of interest. SEER is applicable to even tens of thousands of genomes by counting variable- length k-mers using a distributed string-mining algorithm. Robust options are provided for association analysis that also correct for the clonal population structure of bacteria. Using large collections of genomes of the major human pathogen Streptococcus pneumoniae, SEER identifies relevant previously characterised resistance determinants for several antibiotics.