Velvet - Revision history

Rf at 17:14, 19 December 2016

2016-12-19T17:14:58Z

138.251.175.12 at 09:11, 7 April 2016

2016-04-07T09:11:25Z

Rf at 17:46, 6 April 2016

2016-04-06T17:46:19Z

Rf at 17:32, 6 April 2016

2016-04-06T17:32:29Z

Rf at 17:28, 6 April 2016

2016-04-06T17:28:08Z

Rf: Created page with "This is Daniel Zerbino and Ewan Birney's de-novo genome assembler and is one of the most widely used. It consists of two stages, a hashing stage invoked by the velveth progra..."

2016-03-30T15:34:10Z

Created page with "This is Daniel Zerbino and Ewan Birney's de-novo genome assembler and is one of the most widely used. It consists of two stages, a hashing stage invoked by the velveth progra..."

New page

This is Daniel Zerbino and Ewan Birney's de-novo genome assembler and is one of the most widely used.

It consists of two stages, a hashing stage invoked by the velveth program, and then the actual genome assembly stage
which is invoked by the velvetg program.

As with many other genome assemblers, the program splits short reads into shorter sequences of lenth k, called kmers and
arranges these in de Bruijn graphs from which the genome is then assembled.

← Older revision		Revision as of 17:14, 19 December 2016
Line 12:		Line 12:

	[[File:intleaved.png]]		[[File:intleaved.png]]
		+
		+	= Installation =
		+
		+	Velvet has a few options that are useful to build in at compile time. For colorspace aeembly you will need special executables, ending in "de" and they are compiled with
		+	make color
		+
		+	For allowing a greater variation of kmer sizes (default is a rather lowly 31), ht efollowing compile-time option is avilable.

@@ Line 9: / Line 9: @@
 == input fastq datasets ==
-Velvet differs from other assemblers in requiring that the input short reads, if consisting of pair-end reads be provided within a single file rather than the more usual two files(one for each member of the pair). The two member-reads of each corresponding pair need to follow each other within the file in what may be called an interleaved or shuffled format. The following diagram illustrates the procedure:
+Velvet differs from other assemblers in requiring that the input short reads, if consisting of pair-end reads, be provided within a single file rather than the more usual two files (i.e. one file for each member of the pair). For Velvet, the two member-reads of each corresponding pair need to follow each other within a single file in what may be called an interleaved, or shuffled, format. The following diagram illustrates the procedure:
 [[File:intleaved.png]]

← Older revision		Revision as of 17:46, 6 April 2016
Line 10:		Line 10:

	Velvet differs from other assemblers in requiring that the input short reads, if consisting of pair-end reads be provided within a single file rather than the more usual two files(one for each member of the pair). The two member-reads of each corresponding pair need to follow each other within the file in what may be called an interleaved or shuffled format. The following diagram illustrates the procedure:		Velvet differs from other assemblers in requiring that the input short reads, if consisting of pair-end reads be provided within a single file rather than the more usual two files(one for each member of the pair). The two member-reads of each corresponding pair need to follow each other within the file in what may be called an interleaved or shuffled format. The following diagram illustrates the procedure:
		+
		+	[[File:intleaved.png]]

← Older revision		Revision as of 17:32, 6 April 2016
Line 6:		Line 6:
	As with many other genome assemblers, the program splits short reads into even shorter sequences of length k, called kmers and		As with many other genome assemblers, the program splits short reads into even shorter sequences of length k, called kmers and
	arranges these in de Bruijn graphs from which the genome is then assembled.		arranges these in de Bruijn graphs from which the genome is then assembled.
		+
		+	== input fastq datasets ==
		+
		+	Velvet differs from other assemblers in requiring that the input short reads, if consisting of pair-end reads be provided within a single file rather than the more usual two files(one for each member of the pair). The two member-reads of each corresponding pair need to follow each other within the file in what may be called an interleaved or shuffled format. The following diagram illustrates the procedure:

@@ Line 1: / Line 1: @@
 This is Daniel Zerbino and Ewan Birney's de-novo genome assembler and is one of the most widely used.
-It consists of two stages, a hashing stage invoked by the velveth program, and then the actual genome assembly stage
+It consists of two stages, a hashing stage invoked by the '''velveth''' program, and then the actual genome assembly stage
-which is invoked by the velvetg program.
+which is invoked by the '''velvetg''' program.
-As with many other genome assemblers, the program splits short reads into shorter sequences of lenth k, called kmers and
+As with many other genome assemblers, the program splits short reads into even shorter sequences of length k, called kmers and
 arranges these in de Bruijn graphs from which the genome is then assembled.