pegi3s/velvet repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image facilitates the usage of Velvet⁠, a de novo genome assembler specially designed for short read sequencing technologies.

⁠Using the Velvet image in Linux

You should adapt and run the following command: docker run --rm -v "/your/data/dir:/data" pegi3s/velvet bash -c "velveth /data <k_mer_value> -fastq -short /data/input.fq && velvetg /data -cov_cutoff <coverage_cutoff_value> -min_contig_lgth <minimum_contig_length_value>"

In this command, you should replace:

• /your/data/dir to point to the directory that contains the FASTQ file you want to analyze.
• <k_mer_value> to the value of the k-mer size you want to use.
• <coverage_cutoff_value> to the value of the coverage cutoff you want to use.
• <minimum_contig_length_value> to the value of the minimum contig length you want to use.

For instance, if you want to make an assembly using a k-mer size of 21 with a coverage cutoff of 4 and minimum contig length of 100 base pairs, you should run: docker run --rm -v "/your/data/dir:/data" pegi3s/velvet bash -c "velveth /data 21 -fastq -short /data/input.fq && velvetg /data -cov_cutoff 4 -min_contig_lgth 100"

To see the velveth help, just run docker run --rm pegi3s/velvet velveth --help.

To see the velvetg help, just run docker run --rm pegi3s/velvet velvetg --help.

⁠Using the Velvet image in Windows

Please note that data must be under the same drive than the Docker Toolbox installation (usually C:) and in a folder with write permissions (e.g. C:/Users/User_name/).

You should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/velvet bash -c "velveth /data <k_mer_value> -fastq -short /data/input.fq && velvetg /data -cov_cutoff <coverage_cutoff_value> -min_contig_lgth <minimum_contig_length_value>"