Monthly Archives: September 2015

Qbox

Software @en

General Information

Version: 1.62.3

Qbox is a C++/MPI scalable parallel implementation of first-principles molecular dynamics (FPMD) based on the plane-wave, pseudopotential formalism. Qbox is designed for operation on large parallel computers.

How to use it:

To send qbox jobs to the queue we have created the send_qbox utility_

send_qbox  JOBNAME NODES PROCS_PER_NODE[property] TIME

Executing send_box [Enter] more options will be shown. The program is installed in /software/qbox

More Information

On the Qbox Web page.

IDBA-UD

Genetics, Scientific Software

General information

IDBA-UD 1.1.1 is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions.

How to use

To send jobs to the queue you can use the command

send_idba-ud

which after a few questions configures the job.

Performance

IDBA-UD has a good performance and scaling up to 8 cores. Above we did not measure a improvement. In the benchmark the --mimk 40 --step 20 options has been used. When we have decreased the step the the scalling is worse. This trend can be also seen in the second table.

1 core as base 2 cores as base
Cores Time (s) Speed up Performance (%) Speed up Performance (%)
1 480 1 100
2 296 1.6 81 1.0 100
4 188 2.6 64 1.6 79
8 84 5.7 71 3.5 88
12 92 5.2 43 3.2 54

The second benchark has been done with a bigger file with 10 million bases and the  --mink 20 --step 10 --min_support 2 options. We observe a regular behaviour than in the previous benchmark and how the panellization is good up to 4 cores.

Cores Time (s) Speed up Performance
1 13050 1 100
2 6675 2.0 98
4 3849 3.4 85
8 3113 4.2 52
16 2337 5.6 35
20 2409 5.4 27

More information

IDBA-UD web page.

SPAdes

Genetics, Scientific Software, Uncategorized @en

General information

SPAdes 3.6.0 – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. It 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. 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 single-cell and standard bacterial and fungal data sets.

How to use

To send jobs to the queue you can use the

send_spades

command that asks few questions to configure the job.

Performance

We have not measure any performance improvement or time reduction when using several cores in a standard calculation like:

spades.py -pe1-1 file1 -pe1-2 file2 -o outdir

We recommend to use 1 core, unless you know that you can use better performance with several cores.

More information

Web page of SPAdes.