Ubuntu 20.04 filly contained for MARVEL assembly
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Ubuntu 20.04 fully contained for MARVEL assembly
Find information about the MARVEL assembler here.
I am not part of the developer team - I just made this image.
Copy files from MARVEL example section.
docker run --rm -v $(pwd):/in -w /in chrishah/marvel:e3f3cae gunzip -c /usr/src/MARVEL/examples/e.coli_nanopore/01_Ecoli_K12_R9_1D_Rapid_basecalled.pass.20x.fasta.gz > E_coli.20x.fasta
docker run --rm -v $(pwd):/in -w /in chrishah/marvel:e3f3cae cp /usr/src/MARVEL/examples/e.coli_nanopore/do.py .
Set up initial database with for reads.
docker run --rm -v $(pwd):/in -w /in chrishah/marvel:e3f3cae DBprepare.py ECOL E_coli.20x.fasta
Run assembly (individual steps as detailed in do.py script).
docker run --rm -v $(pwd):/in -w /in chrishah/marvel:e3f3cae python3 ./do.py
Content type
Image
Digest
Size
458 MB
Last updated
over 5 years ago
docker pull chrishah/marvel:e3f3cae