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This article mainly explains "how to install and use velvet". Interested friends may wish to have a look at it. The method introduced in this paper is simple, fast and practical. Let's let the editor take you to learn how to install and use velvet.

Velvet is a genome assembly tool developed by EMBL-EBI.

The installation process is as follows

Wget https://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.10.tgztar xzvf velvet_1.2.10.tgzcd velvet_1.2.10/make 'MAXKMERLENGTH=127'

By default, the maximum length of kmer supported by velvet is 31bp, and if you want a kmer with only a larger length, you need to set the value of MAXKMERLENGTH at compile time. When the compilation is complete, the following two executables are generated

Velveth

Velvetg

The running process of the software is also divided into two steps.

1. Velveth

The usage is as follows

Velveth Assem 31-shortPaired-fasta-separate left.fa right.fa

The first parameter, Assem, represents the directory of the output; shortPaired specifies the sequencing type, and fasta specifies the sequence format of the input.

For the data of the second-generation sequencing platform, the commonly used sequencing types include the following two cases

Short

ShortPaired

Short is used for individual data and shortPaired is used for double-ended data. The imported sequence files support the following formats:

Fasta/fasta.gz

Fastq/fastq.gz

Sam/bam

Specify the format of the input file through different parameters.-fasta corresponds to fasta format;-fastq corresponds to fastq format,-fastq.gz corresponds to fastq.gz format,-fasta.gz corresponds to fasta.gz format,-sam corresponds to sam format, and-bam corresponds to bam format.

For double-ended data, there are two formats

Interleaved

Separate

The R1 and R2 terminal sequences are saved in two files, that is, separate format; interleaved is a format of double-ended sequences, and the R1 and R2 end sequences of each sequence are saved in a file, and the R1 end of each sequence is followed by the R2 terminal sequence; for double-ended sequencing, the default is interleaved format, if it is separate format, the declaration to be displayed.

Another usage that needs to be noted is kmer length, which is usually assembled with a series of kmer lengths in actual analysis, and then selects the best result. The kmer parameter of velvet can be set to a gradient, as shown below

Velveth Assem 31 fasta 37 2-shortPaired-fasta-separate left.fa right.fa

In the above usage, 31 and 37 kmer 2 means that the assembly starts from kmer=31, and then increases step by step, followed by 33, 35, and 37 kmer length assembly. This kind of parameter design is very suitable for the actual needs.

After running, the following files are generated in the output directory

Sequences

Roadmaps

2. Velvetg

The basic usage is as follows

Velvetg Assembly/-min_contig_lgth 100

The first parameter is the output directory of the previous step. Min_contig_lgth represents the minimum length of contig. Contig less than this length will be deleted and will not appear in the final result.

After running, the contigs.fa in the output directory is the final assembly result.

At this point, I believe you have a deeper understanding of "how to install and use velvet". You might as well do it in practice. Here is the website, more related content can enter the relevant channels to inquire, follow us, continue to learn!

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