SSPACE-STANDARD-Teaching
Category
Bioinformatics
Program On
Teaching
Version
3.0
Author / Distributor
Description
" SSPACE-standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data. It is unique in offering the possibility to manually control the scaffolding process. By using the distance information of paired-end and/or mate-pair data, SSPACE is able to assess the order, distance and orientation of your contigs and combine them into scaffolds." More details are at SSPACE-STANDARD
Running Program
The last version of this application is at /usr/local/apps/gb/sspace-standard/3.0
To use this version, please load the module with
ml sspace-standard/3.0
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_SSPACE-STANDARD
#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=SSPACE-STANDARD.%j.out
#SBATCH --error=SSPACE-STANDARD.%j.err
cd $SLURM_SUBMIT_DIR
ml sspace-standard/3.0
perl /usr/local/apps/gb/sspace-standard/3.0/SSPACE_Standard_v3.0.pl [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 sspace-standard/3.0 perl /usr/local/apps/gb/sspace-standard/3.0/SSPACE_Standard_v3.0.pl -h Unknown option: h Usage: /usr/local/apps/gb/sspace-standard/3.0/SSPACE_Standard_v3.0.pl [SSPACE_Standard_v3.0_linux] ============ General Parameters ============ -l Library file containing two mate pate files with insert size, error and either mate pair or paired end indication. -s Fasta file containing contig sequences used for extension. Inserted pairs are mapped to extended and non-extended contigs (REQUIRED) -x Indicate whether to extend the contigs of -s using paired reads in -l. (-x 1=extension, -x 0=no extension, default -x 0) ============ Extension Parameters ============ -m Minimum number of overlapping bases with the seed/contig during overhang consensus build up (default -m 32) -o Minimum number of reads needed to call a base during an extension (default -o 20) ============ Scaffolding Parameters ============ -z Minimum contig length used for scaffolding. Filters out contigs that are below -z (default -z 0 (no filtering), optional). -k Minimum number of links (read pairs) to compute scaffold (default -k 5, optional) -a Maximum link ratio between two best contig pairs *higher values lead to least accurate scaffolding* (default -a 0.7, optional) -n Minimum overlap required between contigs to merge adjacent contigs in a scaffold (default -n 15, optional) ============ Bowtie Parameters ============ -g Maximum number of allowed gaps during mapping with Bowtie. Corresponds to the -v option in Bowtie. *higher number of allowed gaps can lead to least accurate scaffolding* (default -v 0, optional) ============ Additional Parameters ============ -T Specify the number of threads to run SSPACE, used both for reading the input readfiles and mapping the reads against the contigs. For reading in the files, multiple files are read-in simultaneously. With read-mapping, the readmapper is called multiple times with 1 million reads per calls (default -T 1, optional) -S Skip the processing of the reads. Meaning that SSPACE was already run, but user now wants to use different extension/scaffold parameters. -b Base name for your output files (optional) -v Runs the scaffolding process in verbose mode (-v 1=yes, -v 0=no, default -v 0, optional) -p Make .dot file for visualisation (-p 1=yes, -p 0=no, default -p 0, optional) ERROR: Parameter -l is required. Please insert a library file ERROR: Parameter -s is required. Please insert a contig .fasta file
Installation
Source code is obtained from SSPACE-STANDARD
System
64-bit Linux