Lazypipe¶

Description¶

Lazypipe is a Unix pipeline for analyzing Next Generation Sequence (NGS) data. The main emphasis is on assembling, taxonomic binning and taxonomic profiling of bacterial/viral sequences.

Lazypipe is implemented as a collection of Perl, C++, and R programs with a command-line user interface written in Perl. Our implementation allows to execute the entire pipeline with a single command or to perform each analysis step one at a time. This allows for great flexibility when working with large NGS libraries.

Environment Modules¶

Run module spider lazypipe to find out what environment modules are available for this application.

Environment Variables¶

HPC_LAZYPIPE_DIR - installation directory
HPC_LAZYPIPE_BIN - executable directory

Additional Usage 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):

$ 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

Categories¶

genomics