Difference between revisions of "Applications/Centrifuge"
From HPC
m |
(→Batch Job) |
||
| (5 intermediate revisions by the same user not shown) | |||
| Line 3: | Line 3: | ||
==Application Details== | ==Application Details== | ||
| − | * Description: Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive | + | * Description: Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labelling of reads and quantification of species. |
| − | * Version: 1.0.4 | + | * Version: 1.0.4 (and 1.0.4a see text below) |
| − | * Modules: centrifuge/1.0.4 | + | * Modules: centrifuge/1.0.4 and centrifuge/1.0.4a |
* Licence: Open source (Github) | * Licence: Open source (Github) | ||
==Usage Examples== | ==Usage Examples== | ||
| − | [Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive | + | [Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labelling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome). It classifies sequences at a very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers |
| + | |||
| + | * The Centrifuge homepage is http://www.ccb.jhu.edu/software/centrifuge | ||
| + | * The Centrifuge paper is available at https://genome.cshlp.org/content/26/12/1721 | ||
| + | <!--* The Centrifuge poster is available at http://www.ccb.jhu.edu/people/infphilo/data/Centrifuge-poster.pdf--> | ||
| + | |||
| + | |||
| + | centrifuge (1.0.4) is the main GitHub repo with 1.0.4a as the patched version according to | ||
| + | |||
| + | * https://github.com/DaehwanKimLab/centrifuge/commit/a5c09bb29a3a828d88be49c55353cd84b6b9bbad | ||
| + | * https://github.com/DaehwanKimLab/centrifuge/commit/4f2877ca7620d556afd0eff1bee5bfc224b31b7c | ||
| + | |||
<pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
[username@login01 ~]$ module add centrifuge/1.0.4 | [username@login01 ~]$ module add centrifuge/1.0.4 | ||
| + | or | ||
| + | [username@login01 ~]$ module add centrifuge/1.0.4a | ||
| + | </pre> | ||
| + | |||
| + | ===Batch Job=== | ||
| + | <pre> | ||
| + | #!/bin/bash | ||
| + | |||
| + | #SBATCH -J centrifuge | ||
| + | #SBATCH -p compute | ||
| + | #SBATCH -o %N.%j.%a.out | ||
| + | #SBATCH -e %N.%j.%a.err | ||
| + | #SBATCH --exclusive | ||
| + | #SBATCH -t 00:10:00 | ||
| + | |||
| + | module purge | ||
| + | module load centrifuge/1.0.4 | ||
| + | |||
| + | ###Run your commands### | ||
| + | centrifuge-download -o library -d "vertebrate_mammalian" -a "Chromosome" -t 9606,10090 -c 'reference genome' >> seqid2taxid.map | ||
| + | #etc... | ||
</pre> | </pre> | ||
| Line 22: | Line 54: | ||
* [https://github.com/infphilo/centrifuge https://github.com/infphilo/centrifuge] | * [https://github.com/infphilo/centrifuge https://github.com/infphilo/centrifuge] | ||
| − | + | {{Modulepagenav}} | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
Latest revision as of 09:50, 17 November 2022
Application Details
- Description: Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labelling of reads and quantification of species.
- Version: 1.0.4 (and 1.0.4a see text below)
- Modules: centrifuge/1.0.4 and centrifuge/1.0.4a
- Licence: Open source (Github)
Usage Examples
[Centrifuge] is a novel microbial classification engine that enables rapid, accurate and sensitive labelling of reads and quantification of species on desktop computers. The system uses a novel indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.7 GB for all complete bacterial and viral genomes plus the human genome). It classifies sequences at a very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers
- The Centrifuge homepage is http://www.ccb.jhu.edu/software/centrifuge
- The Centrifuge paper is available at https://genome.cshlp.org/content/26/12/1721
centrifuge (1.0.4) is the main GitHub repo with 1.0.4a as the patched version according to
- https://github.com/DaehwanKimLab/centrifuge/commit/a5c09bb29a3a828d88be49c55353cd84b6b9bbad
- https://github.com/DaehwanKimLab/centrifuge/commit/4f2877ca7620d556afd0eff1bee5bfc224b31b7c
[username@login01 ~]$ module add centrifuge/1.0.4 or [username@login01 ~]$ module add centrifuge/1.0.4a
Batch Job
#!/bin/bash #SBATCH -J centrifuge #SBATCH -p compute #SBATCH -o %N.%j.%a.out #SBATCH -e %N.%j.%a.err #SBATCH --exclusive #SBATCH -t 00:10:00 module purge module load centrifuge/1.0.4 ###Run your commands### centrifuge-download -o library -d "vertebrate_mammalian" -a "Chromosome" -t 9606,10090 -c 'reference genome' >> seqid2taxid.map #etc...