DBG2OLC-Teaching: Difference between revisions
(Created page with "Category:TeachingCategory:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Teaching === Version === 20170208 ==...") |
No edit summary |
||
| (3 intermediate revisions by the same user not shown) | |||
| Line 23: | Line 23: | ||
The last version of this application is at /usr/local/apps/eb/DBG2OLC/20170208-foss-2016b | The last version of this application is at /usr/local/apps/eb/DBG2OLC/20170208-foss-2016b | ||
To use this version, please | To use this version, please load the module with | ||
<pre class="gscript"> | <pre class="gscript"> | ||
ml DBG2OLC/20170208-foss-2016b | ml DBG2OLC/20170208-foss-2016b | ||
</pre> | </pre> | ||
Here is an example of a shell script, sub.sh, to run on | Here is an example of a shell script, sub.sh, to run on the batch queue: | ||
<div class="gscript2"> | <div class="gscript2"> | ||
| Line 40: | Line 40: | ||
<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | <nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | ||
<nowiki>#</nowiki>SBATCH --output=DBG2OLC.%j.out<br> | <nowiki>#</nowiki>SBATCH --output=DBG2OLC.%j.out<br> | ||
<nowiki>#</nowiki>SBATCH --error=DBG2OLC.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml DBG2OLC/20170208-foss-2016b<br> | ml DBG2OLC/20170208-foss-2016b<br> | ||
DBG2OLC <u>[options]</u><br> | |||
</div> | </div> | ||
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values. | In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values. | ||
| Line 59: | Line 60: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
ml DBG2OLC/20170208-foss-2016b | 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. | |||
</pre> | </pre> | ||
Latest revision as of 12:19, 15 August 2018
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