DBG2OLC-Teaching
Category
Bioinformatics
Program On
Teaching
Version
20170208
Author / Distributor
Description
"DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies" More details are at DBG2OLC
Running Program
The last version of this application is at /usr/local/apps/eb/DBG2OLC/20170208-foss-2016b
To use this version, please load the module with
ml DBG2OLC/20170208-foss-2016b
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_DBG2OLC
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=DBG2OLC.%j.out
#SBATCH --error=DBG2OLC.%j.err
cd $SLURM_SUBMIT_DIR
ml DBG2OLC/20170208-foss-2016b
DBG2OLC [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml DBG2OLC/20170208-foss-2016b DBG2OLC -h Example command: For third-gen sequencing: DBG2OLC LD1 0 Contigs contig.fa k 17 KmerCovTh 2 MinOverlap 20 AdaptiveTh 0.005 f reads_file1.fq/fa f reads_file2.fq/fa For sec-gen sequencing: DBG2OLC LD1 0 Contigs contig.fa k 31 KmerCovTh 0 MinOverlap 50 PathCovTh 1 f reads_file1.fq/fa f reads_file2.fq/fa Parameters: MinLen: min read length for a read to be used. Contigs: contig file to be used. k: k-mer size. LD: load compressed reads information. You can set to 1 if you have run the algorithm for one round and just want to fine tune the following parameters. PARAMETERS THAT ARE CRITICAL FOR THE PERFORMANCE: If you have high coverage, set large values to these parameters. KmerCovTh: k-mer matching threshold for each solid contig. (suggest 2-10) MinOverlap: min matching k-mers for each two reads. (suggest 10-150) AdaptiveTh: [Specific for third-gen sequencing] adaptive k-mer threshold for each solid contig. (suggest 0.001-0.02) PathCovTh: [Specific for Illumina sequencing] occurence threshold for a compressed read. (suggest 1-3) Author: Chengxi Ye cxy@umd.edu. last update: Jun 11, 2015. Loading contigs. 0 k-mers in round 1. 0 k-mers in round 2. Scoring method: 3 Match method: 1 Loading long read index 0 selected reads. 0 reads loaded.
Installation
Source code is obtained from DBG2OLC
System
64-bit Linux