pilon
automated genome assembly improvement and variant detection tool
Install
- All systems
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curl cmd.cat/pilon.sh
- Debian
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apt-get install pilon - Ubuntu
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apt-get install pilon - Kali Linux
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apt-get install pilon - Windows (WSL2)
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sudo apt-get updatesudo apt-get install pilon - Dockerfile
- dockerfile.run/pilon
pilon
automated genome assembly improvement and variant detection tool
Pilon is a software tool which can be used to: * Automatically improve draft assemblies * Find variation among strains, including large event detection Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including: * Single base differences * Small indels * Larger indel or block substitution events * Gap filling * Identification of local misassemblies, including optional opening of new gaps