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.
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
build/GenomeTailor
SYNOPSIS
build/GenomeTailor -i <input_assembly> -r <input_reads> -m <mode> [-e <output_errors>] [-o
<output_assembly>] [-d <output_non_duplexed_reads>] [-p
<path-to-tmp-folder>] [-b <minimum-number-of-reads>] [-t <threads>] [-g
<gaf_file>] [--minigraph <minigraph>] [--minimap2 <minimap2>] [--racon
<racon>] [--path-to-raven <path-to-raven>] [-h] [-v]
OPTIONS
-i, --input_assembly
input assembly in gfa format
-r, --input_reads
input reads in fasta/q format
-m, --mode mode: correct or detect
-e, --output_errors
output file describing the errors found in the assembly
-o, --output_assembly
output assembly in gfa format (required if correct mode)
-d, --output_non_duplexed_reads
file to output a file of non-duplexed reads
-p, --path-to-tmp-folder
path to a temporary folder where the intermediate files will be stored [./]
-b, --minimum-number-of-reads
minimum number of reads to support a breakpoint [5]
-t, --threads
number of threads to use for minigraph [1]
-g, --gaf_file
gaf file if already computed (NO SECONDARY ALIGNMENTS). Will be generated with
minigraph if not provided
--minigraph path to minigraph
--minimap2 path to minimap2
--racon path to racon
--path-to-raven
path to raven
-h, --help print this help message and exit
-v, --version
print version information and exit