tMHG-Finder is an extension of our previous MHG-Finder package. tMHG-Finder improves our prior work two-fold: (i) it scales to larger bacterial genome datasets, (ii) it provides intermediate MHGs involving subsets of input genomes. tMHG-Finder leverages the MinHash-based alignment-free distance estimator Mash, enabling a fast calculation of pairwise genomic distances between input genomes. Subsequently, neighbor-joining is employed on the distance matrix to sketch a guide tree determining the MHG partition order. Given a guide tree, the MHG partitioning at each internal node involves five steps: (1) BLASTn for pairwise local alignments (2) sequence pile-up (3) initial MHGs and alignment graph construction (4) alignment graph traversal (5) representative sequence calculation
The guide tree used by tMHG-Finder can be either user-provided or auto-estimated. And the final output of tMHG-Finder comprises an MHG set per internal node, which encompasses all taxa located beneath the respective internal node, stored in the directory specified as -tg.
It is highly recommended to setup a new conda environment! Installing MHG via conda will save the time figuring out the dependencies.
conda create --name tmhg bioconda::tmhg
conda activate tmhg
If you are stuck on "solving environment", run conda config --remove channels conda-forge, and then conda config --add channels conda-forge should solve the problem.
But again, it is highly recommend to create a brand new environment.
Using git clone, please install the below dependencies manually:
The following command will install tMHG-Finder an all python dependencies.
python -m pip install .
Additional non-python dependencies are listed below and need to be installed manually. If Anaconda is installed, you can use the installation script for each package directly:
BEDtools
conda install bioconda::bedtools
BLAST
conda install bioconda::blast
MAFFT
conda install bioconda::mafft
Mash
conda install bioconda::mash
$ tmhgf find --help
usage: tmhgf find [-h] [-b BLASTN_DIR] [--mash_tree_path MASH_TREE_PATH] [--customized_tree_path CUSTOMIZED_TREE_PATH] [-r REROOT] [-k KMER_SIZE] [-t THREAD] [-a ALIGNMENT_LENGTH_THRESHOLD] -g GENOME
[-o MHG_OUTPUT_DIR] [-tg TEMP_DIR]
options:
-h, --help show this help message and exit
-b BLASTN_DIR, --blastn_dir BLASTN_DIR
Directory storing blastn results
--mash_tree_path MASH_TREE_PATH
Mash-estimated guide tree path
--customized_tree_path CUSTOMIZED_TREE_PATH
Path to customized tree instead of using auto-estimated tree
-r REROOT, --reroot REROOT
Boolean value determining whether to reroot the guide tree or not. If this is set to True, it will reroot the guide tree changing the MHG output order to minimize the tree height. If this
is False, it will keep the MHG visiting order as it is.
-k KMER_SIZE, --kmer_size KMER_SIZE
Kmer size for Mash, default 16
-t THREAD, --thread THREAD
Number of threads
-a ALIGNMENT_LENGTH_THRESHOLD, --alignment_length_threshold ALIGNMENT_LENGTH_THRESHOLD
Alignment length threshold in base pair. tMHG-Finder does not consider MHGs shorter than 60 base pairs by default. If this threshold is too low, it will result in an excessive amount of
short MHGs and a longer runtime.
-g GENOME, --genome GENOME
Genome nucleotide sequence directory
-o MHG_OUTPUT_DIR, --mhg_output_dir MHG_OUTPUT_DIR
Directory storing all tMHG-Finder outputs
-tg TEMP_DIR, --temp_dir TEMP_DIR
Directory storing a copy of each genome and representative genomes
tMHG-Finder supports adding new genomes or continuing unfinished MHG partitioning using tmhgf add. It first locates the newly added genomes in the new guide tree, and compare the internal node differences between the old guide tree and the new guide tree, and only computes an MHG set for internal nodes which have not yet been computed before to avoid the redundant computation.
$ tmhgf add --help
usage: tmhgf add [-h] [-b BLASTN_DIR] [--mash_tree_path MASH_TREE_PATH] [--customized_tree_path CUSTOMIZED_TREE_PATH] [-r REROOT] [-k KMER_SIZE] [-t THREAD] [-a ALIGNMENT_LENGTH_THRESHOLD] -og OLD_TEMP_GENOME_DIR
-om OLD_MHG_OUTPUT_DIR -g NEW_GENOME_DIR [-o MHG_OUTPUT_DIR] [-tg NEW_TEMP_GENOME_DIR]
options:
-h, --help show this help message and exit
-b BLASTN_DIR, --blastn_dir BLASTN_DIR
Directory storing blastn results
--mash_tree_path MASH_TREE_PATH
Mash-estimated guide tree path
--customized_tree_path CUSTOMIZED_TREE_PATH
Path to customized tree instead of using auto-estimated tree
-r REROOT, --reroot REROOT
Boolean value determining whether to reroot the guide tree or not. If this is set to True, it will reroot the guide tree changing the MHG output order to minimize the tree height. If this
is False, it will keep the MHG visiting order as it is.
-k KMER_SIZE, --kmer_size KMER_SIZE
Kmer size for Mash, default 16
-t THREAD, --thread THREAD
Number of threads
-a ALIGNMENT_LENGTH_THRESHOLD, --alignment_length_threshold ALIGNMENT_LENGTH_THRESHOLD
Alignment length threshold in base pair. tMHG-Finder does not consider MHGs shorter than 60 base pairs by default. If this threshold is too low, it will result in an excessive amount of
short MHGs and a longer runtime.
-og OLD_TEMP_GENOME_DIR, --old_temp_genome_dir OLD_TEMP_GENOME_DIR
Path to the old tMHG-Finder temp genome directory, this is NOT the previous genome directory, but the tMHG-Finder temporary genome directory
-om OLD_MHG_OUTPUT_DIR, --old_mhg_output_dir OLD_MHG_OUTPUT_DIR
Path to the old tMHG-Finder output directory which should contain an MHG set for each internal node
-g NEW_GENOME_DIR, --new_genome_dir NEW_GENOME_DIR
Directory contaning the new set of genomes
-o MHG_OUTPUT_DIR, --mhg_output_dir MHG_OUTPUT_DIR
Directory storing the new MHG output
-tg NEW_TEMP_GENOME_DIR, --new_temp_genome_dir NEW_TEMP_GENOME_DIR
Directory storing a copy of each genome and representative genomes
tmhgf find -g test_data/