LoRDEC processes data coming from high throughput sequencing machines of the second and third generations. These data are called sequencing reads, or simply reads for short. Technically speaking it processes short reads and long reads to correct errors in the long reads.

References:

• Leena Salmela & Eric Rivals LoRDEC: accurate and efficient long read error correction Bioinformatics (2014), Dec 15;30(24):3506-14

• LoRDEC Main Site

This application requires a graphical connection using NX

• Module Name: lordec (see the modules page for more information)
• Some commands are multithreaded

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load lordec

[user@cn3144 ~]$ lordec-correct -2 illumina.fasta -k 19 -s 3 -i pacbio.fasta -o pacbio-corrected.fasta

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. lordec.sh). For example:

#!/bin/bash
set -e
module load lordec
lordec-trim -i corrected.reads.fasta -o trimmed.reads.fasta

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] lordec.sh

Create a swarmfile (e.g. lordec.swarm). For example:

lordec-correct -2 illumina.fasta -k 19 -s 3 -i pacbio_1.fasta -o pacbio_1-corrected.fasta
lordec-correct -2 illumina.fasta -k 19 -s 3 -i pacbio_2.fasta -o pacbio_2-corrected.fasta
lordec-correct -2 illumina.fasta -k 19 -s 3 -i pacbio_3.fasta -o pacbio_3-corrected.fasta
lordec-correct -2 illumina.fasta -k 19 -s 3 -i pacbio_4.fasta -o pacbio_4-corrected.fasta

Submit this job using the swarm command.

swarm -f lordec.swarm [-g #] [-t #] --module lordec