Miniasm assembler can be set up and run by using the Pomoxis package. Pomoxis is a bioinformatics tool designed for processing the nanopore sequencing data.
Q: How to check if the assembler is already installed in my computer?
A: Run the executable. If it shows various flags or options, then it is already installed.
Q: Where is it located or installed in the computer/ What is the path of the assembler’s executable?
A: Run the following command. If it is installed in your computer, it will show the path.
whereis the-name-of-the-executable
Q: Has the executable path been added to the PATH environment variable?
A: Run the following command and check if the executable path is there.
$PATH
Q: Why do you need to add the executable path to the PATH environment variable?
A: You can run the executable in your terminal without having to specifying its path every time.
Q: How do you add the executable path to the PATH environment variable?
A: Run the following command. See https://github.com/asadprodhan/About-the-PATH
export PATH=$PATH:the-path-of-the-executable
Q: How do you install pomoxis?
A: You can install pomoxis using conda. This will also install all the required binaries (i.e. softwares).
conda install -c bioconda pomoxis
Q: What is the pomoxis usage command?
A: Run the following command. It will show all the usage options or flags.
mini_assemble
Q: What will be an example of the pomoxis usage command?
mini_assemble -i sample.fastq -r reference.fasta -o results -p prefix_output_file -t 18
The final assembly will be written to results/test_final.fa