Miniasm-Teaching
Category
Bioinformatics
Program On
Teaching
Version
0.3
Author / Distributor
Description
"Miniasm is a very fast OLC-based de novo assembler for noisy long reads." More details are at miniasm
Running Program
Also refer to Running Jobs on the teaching cluster
- version 0.3, installed in /usr/local/apps/eb/miniasm/0.3-foss-2016b
To use this version of miniasm, please first load the module with
ml miniasm/0.3-foss-2016b
Sample job submission script (sub.sh) to run miniasm in a batch job:
#!/bin/bash
#SBATCH --job-name=j_miniasm
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=2gb
#SBATCH --time=08:00:00
#SBATCH --output=miniasm.%j.out
#SBATCH --error=miniasm.%j.err
cd $SLURM_SUBMIT_DIR
ml miniasm/0.3-foss-2016b
miniasm [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.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
module load miniasm/0.3-foss-2016b miniasm -h miniasm: option requires an argument -- 'h' Usage: miniasm [options] <in.paf> Options: Pre-selection: -R prefilter clearly contained reads (2-pass required) -m INT min match length [100] -i FLOAT min identity [0.05] -s INT min span [2000] -c INT min coverage [3] Overlap: -o INT min overlap [same as -s] -h INT max over hang length [1000] -I FLOAT min end-to-end match ratio [0.8] Layout: -g INT max gap differences between reads for trans-reduction [1000] -d INT max distance for bubble popping [50000] -e INT small unitig threshold [4] -f FILE read sequences [] -n INT rounds of short overlap removal [3] -r FLOAT[,FLOAT] max and min overlap drop ratio [0.7,0.5] -F FLOAT aggressive overlap drop ratio in the end [0.8] Miscellaneous: -p STR output information: bed, paf, sg or ug [ug] -b both directions of an arc are present in input -1 skip 1-pass read selection -2 skip 2-pass read selection -V print version number
Installation
source code from https://github.com/lh3/miniasm/releases
System
64-bit Linux