Skip to content

Latest commit

 

History

History
69 lines (47 loc) · 2.84 KB

jumbodbg_manual.md

File metadata and controls

69 lines (47 loc) · 2.84 KB
Raw

Installation

For installation guide please refer to the installation section of the LJA manual.

Running jumboDBG

Input

Input reads can be in fasta or fastq format and can be compressed using gzip. Make sure that file name extensions correspond to contents of files since they are used to determine file formats. E.g. uncompressed fasta reads are expected to be stored in files with name extensions ".fasta" or ".fa" while compressed fastq reads are expected to be stored in files with name extensions ".fq.gz" or "fastq.gz".

Command line

Here we assume that you added bin subdirectory from installation directory to your PATH variable. Otherwise, you need to use full path to the executable instead of jumboDBG in the command line.

    jumboDBG [options] -o <output_dir> --reads <reads_file> [--reads <reads_file2> ...] -k <int>

Basic options

-o <file_name> (or --output-dir <file_name>) Name of output folder. Resulting graph will be stored there.

-k <int> Value of k (vertex size) to be used for de Bruijn graph construction. k should be odd (otherwise k + 1 is used instead).

--reads <file_name> Name of file that contains reads in fasta or fastq format. This option can be used any number of times in the same command line resulting in collecting reads from multiple files.

--help Print help message.

Advanced options

-t <int> (or --threads <int>) Number of threads. The default value is 16.

-w <int> (or --window <int>) The window size to be used for sparse de Bruijn graph construction. The default value is 2000. Note that all reads of length less than k + w are ignored during graph construction.

--compress Compress all homopolimers in reads.

--coverage Calculate edge coverage of edges in the constructed de Bruijn graph.

Output of de Bruijn graph construction

All output files are stored in <output_dir> `, which is set by the user.

  • <output_dir>/graph.fasta sequences of all edges of de Bruijn graph in fasta format
  • <output_dir>/graph.gfa sequences of all edges of de Bruijn graph in gfa format. Note that gfa format is ill-suited for de Bruijn graph storage since it does not represent some vertices such as vertices with indegree 2 and out degree 0.
  • <output_dir>/graph.dot sequences of all edges of de Bruijn graph
  • <output_dir>/dbg.log log file for the run

Feedback and bug reports

Your comments, bug reports, and suggestions are very welcomed. They will help us to further improve de Bruijn graph construction tool. If you have any trouble running jumboDBG, please send us dbg.log file from the directory <output_dir>.

You can send your comments and bug reports via e-mail: anton.bankevich@gmail.com.