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Installation

Requirements

  • 64 bit Linux OS
  • CMake version 3.1 or above
  • C++ compiler with C++17 support (GCC-7+)
  • GNU make
  • zlib

Downloading and compiling from source code

You can download LJA source code here. To build from source code run the following commands from code directory.

    cmake .
    make

Binary files will be stored in the bin subdirectory. We will further assume that you added bin directory to your PATH variable. Otherwise, you need to use full path to the executable instead of lja in the command line.

Running La Jolla Assembler

Input

Input reads can be in fasta or fastq format and can be compressed using gzip. Make dure that file name extensions correspond to contents of files since they are used to determine file format. 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

To run LJA use the following command line

    lja [options] -o <output_dir> --reads <reads_file> [--reads <reads_file2> ...]

Basic options

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

--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.

-k <int> Value of k (vertex size) to be used for the initial error correction. k should be odd (otherwise k + 1 is used instead).

-K <int> Value of k (vertex size) to be used for the final error correction and initialization of Multiplex de Bruijn graph. K should be odd (otherwise K + 1 is used instead).

--diploid Use this option for diploid genome. By default, LJA assumes that the genome is haploid or inbred.

Output of La Jolla Assembler

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

  • <output_dir>/assembly.fasta final assembly file in fasta format.
  • <output_dir>/mdbg.gfa final multiplex de Bruijn graph in gfa format (experimental feature).
  • <output_dir>/mdbg/assembly.hpc.fasta final assembly file before homopolymer uncompression.
  • <output_dir>/mdbg/mdbg.hpc.gfa final multiplex de Bruijn graph in gfa format with homopolymer compressed edge sequences.
  • <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 La Jolla Assembler. If you have any trouble running LJA, 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.