nanozoo

From: https://github.com/nanoporetech/medaka Command: medaka_consensus

FROM: https://github.com/tseemann/prokka

FROM: https://github.com/Fiware/tools.Md2pdf

from https://github.com/jessieren/DeepVirFinder

From: https://github.com/DaehwanKimLab/centrifuge w/o DB, w stuff to build DB

from https://github.com/rrwick/Unicycler with all dependencies

debian_basic container

from https://github.com/ablab/spades

From Github: ruanjue/wtdbg2 & samtools/samtools & lh3/minimap2

from https://nanoporetech.github.io/pomoxis/index.html

From here: https://github.com/tseemann/abricate

https://github.com/lh3/bwa

From: https://github.com/khyox/recentrifuge incl. database at /database/ncbi_node

https://github.com/samtools/samtools

From: https://github.com/Ecogenomics/CheckM

from here: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Nanopore Assembler https://github.com/ruanjue/wtdbg2

from: https://github.com/dib-lab/sourmash

From here: https://github.com/nanoporetech/ont_tutorial_basicqc

from here https://github.com/marbl/canu

from https://github.com/weizhongli/cdhit incl. blast+ and psi-cd-hit

From here: https://github.com/tseemann/abricate

https://github.com/jts/nanopolish

https://github.com/rrwick/Porechop

Source and Dockerfile from: https://github.com/CSB5/OPERA-MS