Difference between revisions of "Lazypipe"
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An example (assumes the new Lazypipe project is in a folder called /blue/mygroup/share/test_project/ and that the .fastq and host genomes are already in there): | An example (assumes the new Lazypipe project is in a folder called /blue/mygroup/share/test_project/ and that the .fastq and host genomes are already in there): | ||
| + | <div class="mw-collapsible mw-collapsed" style="width:70%; padding: 5px; border: 1px solid gray;"> | ||
| + | ''Expand to view example.'' | ||
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$ cd /blue/mygroup/share/test_project/ | $ cd /blue/mygroup/share/test_project/ | ||
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--inlen 300 \ | --inlen 300 \ | ||
--pipe 1:7,11:13 | --pipe 1:7,11:13 | ||
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<!--Job Scripts--> | <!--Job Scripts--> | ||
Latest revision as of 16:54, 14 December 2022
Description
Lazypipe is a stand-alone pipeline for identifying viruses in host-associated or environmental samples. The main emphasis is on assembling, taxonomic binning and taxonomic profiling of bacterial/viral sequences.
A novel stand-alone pipeline for identifying viruses in host-associated or environmental samples. The Unix based pipeline for automated assembling and taxonomic profiling of NGS libraries has been developed as a collection of C++, Perl and R scripts.
Environment Modules
Run module spider lazypipe to find out what environment modules are available for this application.
System Variables
- HPC_LAZYPIPE_DIR - installation directory
- HPC_LAZYPIPE_BIN - executable directory
Additional Information
When starting a new Lazypipe project, you must initialize the project directory by issuing the command "init_lazypipe_project" from within the new project directory. This will set up the project directory properly to point its resource folders to the application installation directory. This command is only necessary once when you initially create the project directory, but it will not cause any harm if you run it multiple times.
An example (assumes the new Lazypipe project is in a folder called /blue/mygroup/share/test_project/ and that the .fastq and host genomes are already in there):
Expand to view example.
$ cd /blue/mygroup/share/test_project/
$ module load lazypipe/1.2
$ init_lazypipe_project
$ pipeline.pl \
-1 /blue/mygroup/share/test_project/data/M15/M15_R1.fastq \
--hostgen /blue/mygroup/share/test_project/genomes_host/GCA_900108605.1_NNQGG.v01_genomic.fna.gz \
--res /blue/mygroup/share/test_project/results \
--label M15 \
--numth $SLURM_CPUS_PER_TASK \
--inlen 300 \
--pipe 1:7,11:13
Citation
If you publish research that uses lazypipe you have to cite it as follows:
[1] Ilya Plyusnin, Ravi Kant, Anne J. Jaaskelainen, Tarja Sironen, Liisa Holm, Olli Vapalahti, Teemu Smura. (2020) Novel NGS Pipeline for Virus Discovery from a Wide Spectrum of Hosts and Sample Types. Virus Evolution, veaa091, https://doi.org/10.1093/ve/veaa091.