Main tool : dragonflye v1.1.1
dragonflye: Assemble bacterial isolate genomes from Nanopore reads
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
# 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