1.1.1

dragonflye docker image

Main tool : dragonflye v1.1.1

dragonflye: Assemble bacterial isolate genomes from Nanopore reads

Additional tools

Protip: run command docker run staphb/dragonflye:latest micromamba list to see full micromamba environment:

• any2fasta 0.4.2
• assembly-scan 0.4.1
• bwa 0.7.17-r1188
• bcftools 1.15.1
• biopython 1.80
• fastp 0.23.2
• flye 2.9.1
• kmc 3.2.1
• medaka 1.6.1
• miniasm 0.3
• minimap2 2.24-r1122
• nanoq 0.9.0
• perl 5.32.1
• pigz 2.6
• polypolish 0.5.0
• porechop 0.2.4
• python 3.8.15
• racon 1.5.0
• rasusa 0.7.0
• raven 1.8.1
• samclip 0.4.0
• samtools 1.15.1
• seqtk 1.3-r106

Example Usage

# download ONT FASTQs for testing
wget https://raw.githubusercontent.com/bactopia/bactopia-tests/main/data/species/portiera/nanopore/ERR3772599.fastq.gz

# run dragonflye using flye as the assembly algorithm
dragonflye --reads /test/ERR3772599.fastq.gz --prefix ERR3772599-nano.hq --cpus 0 --nopolish --outdir flyehq --gsize 300000 --assembler flye --nanohq