pandaseq
Link to section 'Introduction' of 'pandaseq' Introduction
Pandaseq is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
Docker hub: https://hub.docker.com/r/pipecraft/pandaseq and its home page on Github.
Link to section 'Versions' of 'pandaseq' Versions
- 2.11
Link to section 'Commands' of 'pandaseq' Commands
- pandaseq
Link to section 'Module' of 'pandaseq' Module
You can load the modules by:
module load biocontainers
module load pandaseq
Link to section 'Example job' of 'pandaseq' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run Pandaseq on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=pandaseq
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers pandaseq
pandaseq -f SRR069027_1.fastq -r SRR069027_2.fastq