Difference between revisions of "Quast"

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= Introduction =
 
= Introduction =
  
Quast is a software package that assesses genome assemblies. It is developed by the group that develops SPAdes.
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Quast is a software package that assesses genome assemblies. It is developed by the group that develops SPAdes, so Pavel Pevsner's group at St. Petersburg State University.
  
 
= Usage =
 
= Usage =
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  module load quast
 
  module load quast
  
Quast is installed in the default python installation, so technically, thsi module laod directive is not required. However, it is useful because it loads other modules.
+
Quast is installed in the default python installation, so - technically - this "module load" directive is not required. However, it is useful because it loads other modules and so is recommended.
  
 
An example run:
 
An example run:
  
 
  quast.py test_data/contigs_1.fasta test_data/contigs_2.fasta -R test_data/reference.fasta.gz -G test_data/genes.gff
 
  quast.py test_data/contigs_1.fasta test_data/contigs_2.fasta -R test_data/reference.fasta.gz -G test_data/genes.gff
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 +
<ins>Explanation</ins>:
 +
* the first two arguments are a pair of FASTA files. However these are not paired FASTQ reads, this must be an assembly which happens to be split in two.
 +
* '''-R''' this is for the reference, however it is only optional. IF available, quast can issue more metrics, and without it, less.
 +
* '''-G''' also the tool would like to see genes or features. However if there is no such file, quast can be run before hand as a gene finder. The option '''--gene-finding''' allows this.
  
 
= Installation Notes =
 
= Installation Notes =
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Its '''setup.py''' script is highly customised and does not accept the usual '''--prefix=''' and --install-scripts''' options.
 
Its '''setup.py''' script is highly customised and does not accept the usual '''--prefix=''' and --install-scripts''' options.
The key to installing it in a non-standard location is inserting the right python executable at the head of the '''setup.py''' scritp of the quaast source distribution. I.e for marvin, thsi would be:
+
The key to installing it in a non-standard location is inserting the right python executable at the head of the '''setup.py''' scritp of the quaast source distribution, i.e for marvin, this would be:
  
 
  #!/usr/bin/env python2.7
 
  #!/usr/bin/env python2.7

Latest revision as of 17:30, 14 February 2017

Introduction

Quast is a software package that assesses genome assemblies. It is developed by the group that develops SPAdes, so Pavel Pevsner's group at St. Petersburg State University.

Usage

To load:

module load quast

Quast is installed in the default python installation, so - technically - this "module load" directive is not required. However, it is useful because it loads other modules and so is recommended.

An example run:

quast.py test_data/contigs_1.fasta test_data/contigs_2.fasta -R test_data/reference.fasta.gz -G test_data/genes.gff

Explanation:

  • the first two arguments are a pair of FASTA files. However these are not paired FASTQ reads, this must be an assembly which happens to be split in two.
  • -R this is for the reference, however it is only optional. IF available, quast can issue more metrics, and without it, less.
  • -G also the tool would like to see genes or features. However if there is no such file, quast can be run before hand as a gene finder. The option --gene-finding allows this.

Installation Notes

Quast does not envisage installation into a non-standard directory.

Its setup.py script is highly customised and does not accept the usual --prefix= and --install-scripts options. The key to installing it in a non-standard location is inserting the right python executable at the head of the setup.py scritp of the quaast source distribution, i.e for marvin, this would be:

#!/usr/bin/env python2.7