Speedseq

Description

From the Speedseq Home Page: A flexible framework for rapid genome analysis and interpretation.

Version

0.1.0

Authorized Users

CIRCE account holders
RRA account holders
SC account holders

Platforms

CIRCE cluster
RRA cluster
SC cluster

Modules

Speedseq requires the following module file to run:

apps/speedseq/0.1.0

See Modules for more information.

Running Speedseq on CIRCE/SC

The Speedseq 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.

Interactive Mode

Next, use the following commands to open an SRUN Interactive Session, load the module for Speedseq, and execute the Speedseq binary:

[user@login0 ~]$ srun --time=48:00:00 --nodes=1 --cpus-per-task=1 --pty /bin/bash
[user@wh-520-4-1 ~]$ module load apps/speedseq/0.1.0
[user@wh-520-4-1 ~]$ speedseq align \
    -o NA12878 \
    -R "@RG\tID:NA12878.S1\tSM:NA12878\tLB:lib1" \
    human_g1k_v37.fasta \
    NA12878.1.fq.gz \
    NA12878.2.fq.gz

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 30 minutes to run on a standard PC.

If, for example, you wish to use speedseq align to produce a sorted, duplicate-marked, BAM alignment from paired-end fastq data, you would set up a submit script to use speedseq like this

#!/bin/bash
#
#SBATCH --job-name=speedseq-test
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --output=output.%j.speedseq-test

#### SLURM 1 processor speedseq test to run for 1 hours.

# Load the speedseq module:
module load apps/speedseq/0.1.0

# Start speedseq
speedseq align \
    -o NA12878 \
    -R "@RG\tID:NA12878.S1\tSM:NA12878\tLB:lib1" \
    human_g1k_v37.fasta \
    NA12878.1.fq.gz \
    NA12878.2.fq.gz

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

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./speedseq-test.sh

You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

Speedseq Home Page:
- https://github.com/hall-lab/speedseq

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

Speedseq Annotation files
- /apps/speedseq/0.1.0/annotation
Speedseq Example Script:
- /apps/speedseq/0.1.0/example

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

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