Kallisto-Teaching

Category

Bioinformatics

Program On

Teaching

Version

0.43.1, 0.46.0

Author / Distributor

Nicolas Bray, Harold Pimentel, Páll Melsted and Lior Pachter Kallisto

Description

kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. More information: http://pachterlab.github.io/kallisto/

Running Program

Also refer to Running Jobs on the teaching cluster

Version 0.43.1

• Version 0.43.1, installed in /usr/local/apps/eb/kallisto/0.43.1-foss-2016b

To use this version of kallisto, please first load the module with

module load kallisto/0.43.1-foss-2016b

Version 0.46.0

• Version 0.46.0, installed in /usr/local/apps/eb/kallisto/0.46.0-foss-2018a

To use this version of kallisto, please first load the module with

module load kallisto/0.46.0-foss-2018a

Example of a shell script sub.sh to run kallisto v. 0.46.0 in the batch queue:

#!/bin/bash
#SBATCH --job-name=j_kallisto
#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=kallisto.%j.out
#SBATCH --error=kallisto.%j.err

cd $SLURM_SUBMIT_DIR
ml kallisto/0.46.0-foss-2018a
kallisto <CMD> [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

Example command:

module load kallisto/0.43.1-foss-2016b
kallisto -h

kallisto 0.43.1

Usage: kallisto <CMD> [arguments] ..

Where <CMD> can be one of:

    index         Builds a kallisto index
    quant         Runs the quantification algorithm
    pseudo        Runs the pseudoalignment step
    h5dump        Converts HDF5-formatted results to plaintext
    version       Prints version information
    cite          Prints citation information

Running kallisto <CMD> without arguments prints usage information for <CMD>

module load kallisto/0.46.0-foss-2018a

kallisto

kallisto 0.46.0

Usage: kallisto <CMD> [arguments] ..

Where <CMD> can be one of:

    index         Builds a kallisto index 
    quant         Runs the quantification algorithm 
    bus           Generate BUS files for single-cell data 
    pseudo        Runs the pseudoalignment step 
    merge         Merges several batch runs 
    h5dump        Converts HDF5-formatted results to plaintext
    inspect       Inspects and gives information about an index
    version       Prints version information
    cite          Prints citation information

Running kallisto <CMD> without arguments prints usage information for <CMD>

Installation

Source code from Kallisto

System

64-bit Linux