Quast - Revision history

Rf at 17:30, 14 February 2017

2017-02-14T17:30:44Z

Rf at 17:29, 14 February 2017

2017-02-14T17:29:22Z

Rf at 12:27, 10 February 2017

2017-02-10T12:27:23Z

Rf at 16:43, 9 February 2017

2017-02-09T16:43:12Z

Rf at 17:49, 6 February 2017

2017-02-06T17:49:17Z

Rf at 14:45, 6 February 2017

2017-02-06T14:45:03Z

Rf: Created page with "= Introduction = Quast is a software package that assesses genome assemblies. It is developed by the group that develops SPAdes. = Usage = To load: module load quast An..."

2017-02-06T13:40:36Z

Created page with "= Introduction = Quast is a software package that assesses genome assemblies. It is developed by the group that develops SPAdes. = Usage = To load: module load quast An..."

New page

= Introduction =

Quast is a software package that assesses genome assemblies. It is developed by the group that develops SPAdes.

= Usage =

To load:

module load quast

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

@@ Line 17: / Line 17: @@
 <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 tool would like to see the reference, implying that it is not reference free.
+* '''-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.

← Older revision		Revision as of 17:29, 14 February 2017
Line 14:		Line 14:

	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
		+
		+	<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 tool would like to see the reference, implying that it is not reference free.
		+	* '''-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 =

@@ Line 9: / Line 9: @@
   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:

@@ Line 20: / Line 20: @@
 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

@@ Line 1: / Line 1: @@
 = Introduction =
-Quast is a software package that assesses genome assemblies. It is developed by the group that develops SPAdes.
+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 =