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| # MHG-EVO: _de Novo_ Tree-Based MHG Finder | ||
| # tMHG-Finder: _de Novo_ Tree-Based MHG Finder | ||
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| We are now moving MHG-EVO to conda for an easier installation. | ||
| We are now moving tMHG-Finder to conda for an easier installation. | ||
| \ | ||
| \ | ||
| MHG-EVO is an extension of our previous MHG-Finder package. MHG-EVO improves our prior work two-fold: (i) it scales to larger bacterial genome datasets, (ii) it provides intermediate MHGs involving subsets of input genomes. MHG-EVO 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: | ||
| 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 | ||
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| The guide tree used by MHG-EVO can be either user-provided or auto-estimated. And the final output of MHG-EVO comprises an MHG set per internal node, which encompasses all taxa located beneath the respective internal node, stored in the directory specified as ```-tg```. | ||
| 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```. | ||
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| \ | ||
|  | ||
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| ``` | ||
| MHG-EVO: Guide-Tree Based Homology Group Finder | ||
| usage: tMHG-Finder.py [-h] -g GENOME [-o MHG_OUTPUT_DIR] [-tg TEMP_DIR] [-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] | ||
| tMHG-Finder: Guide-Tree Based Homology Group Finder | ||
| optional arguments: | ||
| -h, --help show this help message and exit | ||
| -g GENOME, --genome GENOME | ||
| Genome nucleotide sequence directory | ||
| -o MHG_OUTPUT_DIR, --mhg_output_dir MHG_OUTPUT_DIR | ||
| Directory storing all MHG-EVO outputs | ||
| Directory storing all tMHG-Finder outputs | ||
| -tg TEMP_DIR, --temp_dir TEMP_DIR | ||
| Directory storing a copy of each genome and | ||
| representative genomes | ||
| Directory storing a copy of each genome and representative | ||
| genomes | ||
| -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 | ||
| 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. | ||
| 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. MHG-EVO 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. | ||
| 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. | ||
| ``` | ||
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| MHG-EVO supports adding new genomes or continuing unfinished MHG partitioning using ```mhg-evo-add-genome```. 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. | ||
| tMHG-Finder supports adding new genomes or continuing unfinished MHG partitioning using ```tMHG-Finder-add-genome```. 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. | ||
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| ``` | ||
| mhg-evo-add-genome: add new genomes to an already partitioned set of existing | ||
| usage: tMHG-Finder-add-genome.py [-h] -og OLD_TEMP_GENOME_DIR -om OLD_MHG_OUTPUT_DIR -g | ||
| NEW_GENOME_DIR [-o MHG_OUTPUT_DIR] | ||
| [-tg NEW_TEMP_GENOME_DIR] [-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] | ||
| tMHG-Finder:-add-genome: add new genomes to an already partitioned set of existing | ||
| genomes | ||
| optional arguments: | ||
| -h, --help show this help message and exit | ||
| -og OLD_TEMP_GENOME_DIR, --old_temp_genome_dir OLD_TEMP_GENOME_DIR | ||
| Path to the old mhg-evo temp genome directory, this is | ||
| NOT the previous genome directory, but the mhg-evo | ||
| temporary genome directory | ||
| 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 MHG-EVO output directory which should | ||
| contain an MHG set for each internal node | ||
| 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 | ||
| Directory storing a copy of each genome and representative | ||
| genomes | ||
| -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 | ||
| 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. | ||
| 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. MHG-EVO 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. | ||
| 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. | ||
| ``` | ||
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| ## Testing Case | ||
| ``` | ||
| python3 mhg-evo.py -g test_data/ | ||
| python3 tMHG-Finder.py -g test_data/ | ||
| ``` | ||
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