SpeedSeq 0.1.2

SpeedSeq is an open-source genome analysis platform that accomplishes alignment, variant detection and functional annotation of a 50× human genome in 13 h on a low-cost server and alleviates a bioinformatics bottleneck that typically demands weeks of computation with extensive hands-on expert involvement. SpeedSeq offers performance competitive with or superior to current methods for detecting germline and somatic single-nucleotide variants, structural variants, insertions and deletions, and it includes novel functionality for streamlined interpretation.

Accessing the software

To load the module:

$ module load speedseq/0.1.2-foss-2016.10-Python-2.7.11

An example command to include in your job script:

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

This is for FASTQ files named NA12878. Other example workflows can be found on their Github page.

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations

None.

Other Information

The Support Level for this application is An.

Visit the Github repository for more information regarding this application.


Last modified: 5 March 2018