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.
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.
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
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