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SPAdes

Main tool: SPAdes

SPAdes genome assembler

Example commands

# 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