pegi3s/hisat2 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 HISAT2⁠, a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA).

The main commands available are hisat2, hisat2-build, and hisat2-inspect. To see hisat2 options, just run docker run --rm pegi3s/hisat2 hisat2 --help.

⁠Using the HISAT2 image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/hisat2 <hisat2_cmd> <options>

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input files you want to analyze.
• <hisat2_cmd> to the name of the HISAT2 command you want to use (hisat2, hisat2-build, or hisat2-inspect).
• <options> with the specific options of the command. These options will include the input/output files, which should be referenced under /data/.

⁠Examples

⁠Example 1: paired-end reads alignment

For instance, if you want to generate a high quality VCF file from an input SAM file, you should run the following three steps:

DATA_DIR=/your/data/dir

docker run --rm -v ${DATA_DIR}:/data pegi3s/hisat2 hisat2 \
    -x /data/hisat2-indexes/genome_index \
    -1 /data/hcc1395_normal_rep1_1.fastq.gz \
    -2 /data/hcc1395_normal_rep1_1.fastq.gz \
    -S /data/output.sam

To test the previous commands, the input files available here⁠.

⁠Using the HISAT2 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/).

As in the Linux case, to run an application, you should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/hisat2 <hisat2_cmd> <options>