Miniasm-Teaching

Category

Bioinformatics

Program On

Teaching

Version

0.3

Author / Distributor

miniasm

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 

#PBS -S /bin/bash
#PBS -N j_miniasm
#PBS -q batch
#PBS -l nodes=1:ppn=1
#PBS -l walltime=120:00:00
#PBS -l mem=20gb

cd $PBS_O_WORKDIR
module load miniasm/0.3-foss-2016b
time miniasm [options]

where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, and the job name need to be modified appropriately as well.

Example of job submission

qsub  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

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Installation

source code from https://github.com/lh3/miniasm/releases

System

64-bit Linux