parsnp
rapid core genome multi-alignment
Install
- All systems
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curl cmd.cat/parsnp.sh
- Debian
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apt-get install parsnp - Ubuntu
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apt-get install parsnp - Kali Linux
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apt-get install parsnp - Windows (WSL2)
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sudo apt-get updatesudo apt-get install parsnp - Raspbian
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apt-get install parsnp - Dockerfile
- dockerfile.run/parsnp
parsnp
rapid core genome multi-alignment
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 includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.