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GenomeTailor

GenomeTailor edits the assembly graph in GFA format to make sure all reads align end-to-end on the graph. It also deletes the regions that are not covered by any reads. Currently under development and not very stable, if you need to perfect your assemblies I advise you write to me.

Installation

Dependencies

To compile the project you will need CMake>=3.8.12 and GCC (tested with GCC=11.3.1). You will need to have racon, minimap2, raven and optionnally minigraph.

Download & install

git clone https://github.com/RolandFaure/GenomeTailor.git
cd GenomeTailor
mkdir build && cd build
cmake ..
make

Test the installation on the test instance:

cd test
../build/GenomeTailor -i assembly.gfa -r mock_reads.fasta -o test.gfa

Usage

SYNOPSIS
        build/GenomeTailor -i <input_assembly> -r <input_reads> -o <output_assembly> [-g <gaf_file>]
                           [-n <minigraph>] [-m <minimap2>] [-r <racon>] [-h] [-v]

OPTIONS
        -i, --input_assembly
                    input assembly in gfa format

        -r, --input_reads
                    input reads in fasta/q format

        -o, --output_assembly
                    output assembly in gfa format

        -g, --gaf_file
                    gaf file. Will be generated with minigraph if not provided

        -n, --minigraph
                    path to minigraph

        -m, --minimap2
                    path to minimap2

        -r, --racon path to racon
        -h, --help  print this help message and exit
        -v, --version
                    print version information and exit