SPAdes (St. Petersburg genome assembler)  is a de novo genome assembly toolkit containing various assembly pipelines; version 3.15.5 was released on July 14th, 2022.

The current version of SPAdes works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. One can also provide additional contigs that will be used as long reads. SPAdes supports paired-end reads, mate-pairs and unpaired reads. The authors note: SPAdes is not intended for larger genomes (e.g. mammalian size genomes). For such purposes you can use it at your own risk.

If you have high-coverage data for bacterial/viral isolate or multi-cell organism, the authors recommend you use the --isolate option.

Read data files can be quite large. If you have large read files, we recommend using the Globus file transfer mechanism, which is robust, resunmable, and it will let you keep working while your files upload.

Manual for SPAdes

SPAdes Q and A forum

SPAdes home page here.

INPUT = reads must be in fastq.gz format only.
The SPAdes implementation on CIPRES is a little non-intuitive. You just choose one of the read files (e.g. R1) as primary input when creating the job, and the parameter pane in the interface will allow you to add any other read files that are required.

This is a new offering, so please report any issues you find.

Simple Example of Run Input/Output

Input File Type File Name
Read file R1 (fastq.gz files only!!) spades_inputfastq_R1.sub.fq.gz
Read file R2 (fastq.gz files only!!) spades_inputfastq_R2.sub.fq.gz
Output File Type File Name
log file spades.log
All output in a zipped directory (large)

If you use SPAdes, please cite: Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A., & Korobeynikov, A. (2020). Using SPAdes de novo assembler. Current Protocols in Bioinformatics, 70, e102. doi: 10.1002/cpbi.102

If there is a tool or a feature you need, please let us know.

hummingbird in flight

Get 1000 Hours free

On the UCSD Supercomputer

Start Your Trial