spades

De novo genome sequence assembler for single-cell and isolate genomes

brewmacoslinux

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De novo genome sequence assembly

spades.py

Assemble paired-end reads from Illumina sequencing$ spades.py -1 reads_R1.fastq -2 reads_R2.fastq -o assembly_output

Assemble single-end reads with specified k-mer sizes$ spades.py -s reads.fastq -k 21,33,55,77 -o assembly_output

Perform single-cell assembly with automatic parameters$ spades.py --sc -1 reads_R1.fastq -2 reads_R2.fastq -o assembly_output