Difference between revisions of "Velvet"
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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. | ||
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| + | == input fastq datasets == | ||
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| + | 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: | ||
Revision as of 17:32, 6 April 2016
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 even shorter sequences of length k, called kmers and 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:
