Main tool: SPAdes
SPAdes genome assembler
Additional tools:
- python 3.8.10
# Test with supplied E. coli data
docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data staphb/spades:latest spades.py --test
# paired-end Illumina reads are in the $PWD
$ ls
SRR7062227_1.fastq.gz SRR7062227_2.fastq.gz
# assemble with your own data (broken into two lines for readability)
docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data staphb/spades:latest \
spades.py -1 /data/SRR7062227_1.fastq.gz -2 /data/SRR7062227_2.fastq.gz -t 8 --isolate -o /data/SRR7062227-spades-output/View full spades help options: docker run --rm -u $(id -u):$(id -g) -v ${PWD}:/data staphb/spades:latest spades.py --help