SPAdes

Description

From the SPAdes Home Page: SPAdes is an assembly toolkit containing various assembly pipelines. SPAdes works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. You can also provide additional contigs that will be used as long reads. SPAdes supports paired-end reads, mate-pairs and unpaired reads. SPAdes can take as input several paired-end and mate-pair libraries simultaneously. Note, that SPAdes was initially designed for small genomes. It was tested on bacterial (both single-cell MDA and standard isolates), fungal and other small genomes. SPAdes is not intended for larger genomes (e.g. mammalian size genomes). For such purposes you can use it at your own risk.


Version

  • 3.11.1

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

SPAdes requires the following module file to run:

  • apps/spades/3.11.1

Running SPAdes on CIRCE/SC

The SPAdes user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Batch Job submission

To run batch jobs on the CIRCE/SC cluster, users will need to submit their jobs to the scheduling environment if their jobs take more than 20 minutes to run on a standard PC.

If, for example, you want to start a job using the toy data set from the SPAdes manual, you would set up a submit script to use spades like this:

[user@login0 ~]$ cd my/jobdir
[user@login0 ~]$ vi spades_test.sh


NOTE: vi can be replaced by the text editor of your choice.

#!/bin/bash
#
#SBATCH --job-name=spades_test
#SBATCH --time=02:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --mem-per-cpu=2048
#SBATCH --output=spades_test-%j.out

#### SLURM single processor spades test to run for 2 hours with 2 GB of memory.

# Load the spades module:
module load apps/spades/3.11.1

# Start spades python script
spades.py --pe1-1 ./ecoli_1K_1.fq.gz --pe1-2 ecoli_1K_2.fq.gz -o spades_test

 
Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 jobdir]$ sbatch ./spades_test.sh


You can view the status of your job with the “squeue -u <username>” command. The toy data used for the example can be found in

  • /apps/spades/3.11.1/share/spades/test_dataset/

Documentation

Home Page, User Guides, and Manuals

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with SPAdes to the IT Help Desk: rc-help@usf.edu