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conda create --name komb-env python=3.9
conda config --add channels conda-forge
conda config --add channels bioconda

conda install bwa-mem2
conda install seqkit
conda install igraph>=0.10.0

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
rustup toolchain install nightly
git clone https://github.com/algbio/ggcat --recursive
cd ggcat/
cargo install --path crates/cmdline/ --locked

git clone https://gitlab.com/treangenlab/komb.git.
cd komb 
./autogen.sh
./configure
make; make install

usage: KOMB.py [-h] -i INPUT_READS1 -j INPUT_READS2 [-o OUTPUT_DIR] [--keep-alignments] [-e LOG_FILE] [--overwrite] -k KMER_SIZE [-t NUM_THREADS] [-l MIN_UNITIG_LENGTH] [-v VERBOSITY] [-c MIN_COUNT]
               [-m GGCAT_MEMORY] [--eulertigs | --greedy-matchtigs | --pathtigs] [--min-seed-length MIN_SEED_LENGTH]

KOMB Analysis Pipeline example: python KOMB.py -i <read1.fq> -j <read2.fq> -k <k-mer size> -t <threads>

optional arguments:
  -h, --help            show this help message and exit
  --eulertigs           Generate Eulertigs instead of unitigs
  --greedy-matchtigs    Generate greedy matchtigs instead of unitigs
  --pathtigs            Generate pathtigs instead of unitigs

Input/Output:
  -i INPUT_READS1, --input-reads1 INPUT_READS1
                        Path to the first sequencing reads file for paired-end data in FASTQ format
  -j INPUT_READS2, --input-reads2 INPUT_READS2
                        Path to the second sequencing reads file for paired-end data in FASTQ format
  -o OUTPUT_DIR, --output-dir OUTPUT_DIR
                        Path to the first sequencing reads file for paired-end data in FASTQ format
  --keep-alignments     Keep SAM files after the graph has been constructed (might require a lot of disk space)
  -e LOG_FILE, --log-file LOG_FILE
                        File for logging [default: stdout]
  --overwrite           Delete <output-dir> and create a new one in case it exists

Common arguments:
  -k KMER_SIZE, --kmer-size KMER_SIZE
                        k-mer size used for the *tig construction and subsequent analyses
                        use -1 to let KOMB automatically pick a value [default: -1]
  -t NUM_THREADS, --num-threads NUM_THREADS
                        Maximum number of threads you want programs to use, note that some might use less than the amount specified
  -l MIN_UNITIG_LENGTH, --min-unitig-length MIN_UNITIG_LENGTH
                        Minimum length of a unitig to be kept for the analysis.
                        Value -1 indicates setting this to the read length [default]
                        Value 0 would result in keeping all unitigs, and values > 0 will apply the filter
  -v VERBOSITY, --verbosity VERBOSITY
                        Logging level: 0 (DEBUG), 1 (INFO), 2 (ERROR)

GGCAT *tig construction:
  -c MIN_COUNT, --min-count MIN_COUNT
                        Minimum count required to keep a kmer [default: 2]
  -m GGCAT_MEMORY, --ggcat-memory GGCAT_MEMORY
                        Maximum memory usage for GGCAT (GB) [default: 8]

BWA MEM parameters:
  --min-seed-length MIN_SEED_LENGTH
                        Minimum seed length. Matches shorter than the value will be missed.