GapFiller-Teaching: Difference between revisions
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<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | <nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br> | ||
<nowiki>#</nowiki>SBATCH --output=GapFiller.%j.out<br> | <nowiki>#</nowiki>SBATCH --output=GapFiller.%j.out<br> | ||
<nowiki>#</nowiki>SBATCH --error=GapFiller.%j.err<br> | |||
cd $SLURM_SUBMIT_DIR<br> | cd $SLURM_SUBMIT_DIR<br> | ||
ml GapFiller/2.1.1-foss-2016b<br> | ml GapFiller/2.1.1-foss-2016b<br> | ||
GapFiller <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. | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
ml GapFiller/2.1.1-foss-2016b | ml GapFiller/2.1.1-foss-2016b | ||
GapFiller --help | |||
GapFiller version 2.1.1 | |||
Allowed options | |||
--help produce help message | |||
--k arg length of the word used to hash (default: 12) | |||
--block-length arg length of perfect match (default: 15) | |||
--output-prefix arg output files prefix (default: "GapFiller_output") | |||
--gz compress output with gzip | |||
--bz2 compress output with bzip2 | |||
--seed1 arg seed1 fasta file (can be compressed with gzip or bzip2, | |||
or a pipe) | |||
--seed2 arg seed2 fasta file (can be compressed with gzip or bzip2, | |||
or a pipe) | |||
--seed-sam arg seed sam file sorted by ID, with header (sam or bam | |||
format; can be repeated multiple times) | |||
--query arg query fasta file: use different reads for extension | |||
instead of seeds (can be compressed with gzip or bzip2, | |||
or a pipe) | |||
--query-sam arg query sam file: use different reads for extension | |||
instead of sam seeds (sam or bam format; can be | |||
repeated multiple times) | |||
--seed-ins arg seed reads insert size | |||
--seed-var arg seed reads insert variation | |||
--store-layout store contigs layout (default: false) | |||
--overlap arg minimum suffix-prefix overlap (default: 30) | |||
--mismatch-rate arg maximum number of mismatches every 100 bp (default: 5) | |||
--extThreshold arg number of reads needed to extend a contig (default: 2) | |||
--limit arg limits the number of extended reads (useful for tests) | |||
--no-read-cycle allow reads to be used multiple times within the same | |||
contig (default: false) | |||
--mate-pairs default: paired-ends | |||
--verbose print a lot of information! Use with --limit option | |||
</pre> | </pre> |
Latest revision as of 15:16, 10 August 2018
Category
Bioinformatics
Program On
Teaching
Version
2.1.1
Author / Distributor
Description
"GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. It can be used for both DNA and RNA and it has been tested on Illumina data." More details are at GapFiller
Running Program
The last version of this application is at /usr/local/apps/eb/GapFiller/2.1.1-foss-2016b
To use this version, please load the module with
ml GapFiller/2.1.1-foss-2016b
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_GapFiller
#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=GapFiller.%j.out
#SBATCH --error=GapFiller.%j.err
cd $SLURM_SUBMIT_DIR
ml GapFiller/2.1.1-foss-2016b
GapFiller [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 GapFiller/2.1.1-foss-2016b GapFiller --help GapFiller version 2.1.1 Allowed options --help produce help message --k arg length of the word used to hash (default: 12) --block-length arg length of perfect match (default: 15) --output-prefix arg output files prefix (default: "GapFiller_output") --gz compress output with gzip --bz2 compress output with bzip2 --seed1 arg seed1 fasta file (can be compressed with gzip or bzip2, or a pipe) --seed2 arg seed2 fasta file (can be compressed with gzip or bzip2, or a pipe) --seed-sam arg seed sam file sorted by ID, with header (sam or bam format; can be repeated multiple times) --query arg query fasta file: use different reads for extension instead of seeds (can be compressed with gzip or bzip2, or a pipe) --query-sam arg query sam file: use different reads for extension instead of sam seeds (sam or bam format; can be repeated multiple times) --seed-ins arg seed reads insert size --seed-var arg seed reads insert variation --store-layout store contigs layout (default: false) --overlap arg minimum suffix-prefix overlap (default: 30) --mismatch-rate arg maximum number of mismatches every 100 bp (default: 5) --extThreshold arg number of reads needed to extend a contig (default: 2) --limit arg limits the number of extended reads (useful for tests) --no-read-cycle allow reads to be used multiple times within the same contig (default: false) --mate-pairs default: paired-ends --verbose print a lot of information! Use with --limit option
Installation
Source code is obtained from GapFiller
System
64-bit Linux