Note (Help Messages): a -h flag after a command (e.g. >structural_pangenome find-ngaps -h) generates a help message for said command.
>structural_pangenome --help displays available structural_pangenome commands.
Step1: Ngap detection
Description | Report the stretch of Ns (Ngap) in each assembly |
Command | structural_pangenome find-ngaps assembly_fasta_file -o output_file OR structural_pangenome find-ngaps assembly_fasta_file -p prefix_folder |
haptic command | haptic find-ngaps assembly_fasta_file_file -o output_file OR haptic find-ngaps assembly_fasta_file_file -p prefix_folder |
Parameters | o: output filename (with complete path) p: prefix_folder which stores the resulting output file. t: optional parameter, threshold: minimum recurrence of Ngap sequence length that affects statistics (integer) |
Input | Fasta file for each assembly (FILE) |
output | Ngap.bed file for each assembly (OUTPUT) |
| Usage | structural_pangenome find-ngaps [-h] (-p PREFIX | -o OUTPUT) [-t THRESHOLD] FILE |
Example | structural_pangenome find-ngaps fastas/assembly_1.fas -o outputs/1.Ngaps/resulting_ngaps.bed |
| haptic example | haptic find-ngaps fastas/assembly_1.fas -o outputs/resulting_ngaps.bed |
Can be Parallelized | Yes |
Optional | No |
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| Description | Extract from minigraph pangenome all fragmented sequences in a FASTA file |
| Command | structural_pangenome convert gfa2fa assembly_1_2_3.gfa > -o 2.3.Stat/pangenome__fasta.fas |
| Parameters | gfa2fa: convert GFA file to FASTA file |
| Input | One gfa file for all assemblies (GFA) |
| Output | One FASTA file for the whole pangenome (OUTPUT) |
| Usage | structural_pangenome convert gfa2fa GFA > -o OUTPUT |
| Example | structural_pangenome convert gfa2fa 2.2.gfas/assembly123.gfa > -o 2.3.Stat/pangenome__fasta.fas |
| Parallelizable | No |
| Optional | No |
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Description | Get the pangenome sequence length distribution |
Command | structural_pangenome find-seqlen pengenome_fasta_file -o output_file OR structural_pangenome find-seqlen pengenome_fasta_file -p prefix_folder |
| haptic command | haptic find-seqlen pengenome_fasta_file -o output_file OR haptic find-seqlen pengenome_fasta_file -p prefix_folder |
Parameters | o: output filename (with complete path) (OUTPUT) p: prefix_folder which stores the resulting output file (with complete path) (PREFIX) g: optional parameter which also displays a graph of the sequence length distribution (-g) |
Input | Fasta file for each assembly (FILE) |
output | One csv file for the whole Pangenome (OUTPUT) |
| Usage | structural_pangenome find-seqlen [-h] (-p PREFIX | -o OUTPUT) [-g] FILE |
Example | structural_pangenome find-seqlen pangenomes/pangenome__fasta.fas -o outputs/2.4.PangSeqLen/pangenome_seqlen.csv -g |
| haptic example | haptic find-seqlen pangenomes/pangenome__fasta.fas -o outputs/pangenome_seqlen.csv |
Can be Parallelized | No |
Optional | Yes |
...
Description | Compare Assembly vs pangenome |
Command | structural_pangenome indexed_assembly_fasta_file pangenome_fasta_file -o output_file OR structural_pangenome align indexed_assembly_fasta_file pangenome_fasta_file -p prefix_folder |
| haptic command | haptic align indexed_assembly_fasta_file pangenome_fasta_file -o output_file OR haptic align indexed_assembly_fasta_file pangenome_fasta_file -p prefix_folder |
Parameters | o: output filename (with complete path) p: prefix_folder which stores the resulting output file (with complete path) |
Input | Indexed fasta file for each assembly (TARGET) - From Step2.1, and the Pangenome Fasta file (QUERY) , it will be shared separately - From Step2.3 |
output | Pangenome paf file (OUTPUT) |
| Usage | structural_pangenome align [-h] (-p PREFIX | -o OUTPUT) TARGET QUERY |
Example | structural_pangenome align fastas/assembly_1_indexed.fas pangenome/pangenome__fasta.fas -o outputs/output_pangenome.paf |
| haptic example | haptic align fastas/assembly_1_indexed.fas pangenome/pangenome__fasta.fas -o outputs/output_pangenome.paf |
Can be Parallelized | Yes |
Optional | No |
...
Description | Convert the PAF file into a delta file. |
Command | structural_pangenome convert paf2delta paf_file assembly__fasta pangenome__fasta -o output_file OR structural_pangenome convert paf2delta paf_file assembly__fasta pangenome__fasta -p prefix_folder |
| haptic command | haptic convert paf2delta paf_file assembly__fasta pangenome__fasta -o output_file OR haptic convert paf2delta paf_file assembly__fasta pangenome__fasta -p prefix_folder |
Parameters | o: output filename (with complete path) p: prefix_folder which stores the resulting output file (with complete path) |
Input |
|
output | Assembly Delta File (OUTPUT) |
| Usage | structural_pangenome convert paf2delta structural_pangenome convert paf2delta FILE TARGET QUERY [-h] (-p PREFIX | -o OUTPUT) |
Example | structural_pangenome convert paf2delta pafs/assembly_1_vs_pangenome__fasta.paf fastas/assembly_1.fas pangenomes/pangenome__fasta.fas -p outputs/paf2delta |
| haptic example | haptic convert paf2delta pafs/assembly_1_vs_pangenome__fasta.paf fastas/assembly_1.fas pangenomes/pangenome__fasta.fas -p outputs/paf2delta |
Can be Parallelized | Yes |
Optional | No |
...
Description | OPTIONAL dotplot of the WGA |
Command | structural_pangenome render-dotplot delta_file -o output_file OR structural_pangenome render-dotplot delta_file -p prefix_folder |
| haptic command | haptic render-dotplot delta_file -o output_file OR haptic render-dotplot delta_file -p prefix_folder |
Parameters | o: output filename (with complete path) (OUTPUT) p: prefix_folder which stores the resulting output file (with complete path) (PREFIX) |
Input | Assembly fasta delta file (DELTA) - From Step3. |
output | · Assembly Fasta gp file · Assembly Fasta rplot file · Assembly Fasta fplot file · Assembly Fasta PNG file |
| Usage | structural_pangenome render-dotplot [-h] (-p PREFIX | -o OUTPUT) DELTA |
Example | structural_pangenome render-dotplot Step3.deltas/assembly_1_vs_pangenome__fasta.delta -p outputs/dotplotStep4.Render |
| haptic example | haptic render-dotplot deltas/assembly_1_vs_pangenome__fasta.delta -p outputs/dotplot |
Can be Parallelized | Yes |
Optional | Yes |
...
| Description | Filter the minimap2 result (filter unwanted regions from delta file) |
| Command | structural_pangenome filter-delta assembly_1_vs_pangenome__fasta.delta |
| Parameters | o: output filename (with complete path) (OUTPUT) p: prefix_folder which stores the resulting output file (with complete path) (PREFIX) m: optional, metrics: save filtering metrics to a file (name auto-generated) --inner_cutoff: optional, (INNER_CUTOFF): Threshold to filter the delta results based on the in between two existing fragments. default value: 0.8 --outer_cutoff: optional, (OUTER_CUTOFF): Threshold to filter the delta results based on the overlap with another fragment. default value: 0.5 |
| Input | Assembly Delta File - From Step3. |
| output | Filtered Assembly Delta File |
| Usage | structural_pangenome filter-delta [-h] (-p PREFIX | -o OUTPUT) FILE [-INNER_CUTOFF] [-OUTER_CUTOFF] [-m] |
| Example | structural_pangenome filter-delta deltas/assembly_1_vs_pangenome__fasta.delta -o filtered_deltas/ssembly_1_vs_pangenome__fasta_bbmh_filter.delta -m |
| Can be Parallelized | Yes |
| Optional | No |
...
Description | OPTIONAL dotplot of the WGA |
Command | structural_pangenome render-dotplot filtered_delta_file -o output_file OR structural_pangenome render-dotplot filtered_delta_file -p prefix_folder |
| haptic command | haptic render-dotplot filtered_delta_file -o output_file OR haptic render-dotplot filtered_delta_file -p prefix_folder |
Parameters | o: output filename (with complete path) (PREFIX) p: prefix_folder which stores the resulting output file (with complete path) (OUTPUT) |
Input | Assembly fasta filtered delta file (DELTA) - From Step5. |
output | · Assembly Fasta gp file · Assembly Fasta rplot file · Assembly Fasta fplot file · Assembly Fasta PNG file |
| Usage | structural_pangenome render-dotplot [-h] (-p PREFIX | -o OUTPUT) DELTA |
Example | structural_pangenome render-dotplot deltas/assembly_1_vs_pangenome__fasta_bbmhFilter.delta -p outputs/dotplot |
| haptic example | haptic render-dotplot deltas/assembly_1_vs_pangenome__fasta_bbmhFilter.delta -p outputs/dotplot |
Can be Parallelized | Yes |
Optional | Yes |
...
| Description | y |
| Command | structural_pangenome reverse-delta assembly_1_vs_pangenome__fasta_bbmhFilter.delta -o pangenome__fasta_vs_assembly_1_bbmhFilter.delta |
| Parameters | o: output filename (with complete path) (PREFIX) p: prefix_folder which stores the resulting output file (with complete path) (OUTPUT) |
| Input | Assembly fasta filtered delta file (FILE) - From Step6. |
| output | Reverse filtered delta file (OUTPUT) |
| Usage | structural_pangenome reverse-delta [-h] (-p PREFIX | -o OUTPUT) FILE |
| Example | structural_pangenome reverse-delta filtered_deltas/_assembly1_v1_bbmh-filter.delta -o reversed_filtered_deltas/ pangenome__fasta_vs_assembly_1_bbmhFilter.delta |
| Can be parallelized | Yes |
| Optional | No |
...
Description | Create the coordinate pangenome system in JSON |
Command | structural_pangenome build-coordinate reverse_filtered_delta_file -o output_file OR structural_pangenome build-coordinate delta_file -p prefix-folder |
| haptic command | haptic build-json reverse_filtered_delta_file -o output_file OR haptic build-json delta_file -p prefix-folder |
Parameters | o: output filename (with complete path) p: prefix_folder which stores the resulting output file (with complete path) unzipped, optional: set this flag to generated an uncompressed file (–unzipped) pretty, optional: set this flag to generated a json file that is human readable (–pretty) m, optional: metrics, Whether to save coordinate metrics. Filename auto-generated if not given (-m) |
Input | Reversed filtered delta file(s) (DELTA) (DELTA ..), - From Step7. |
output | Pangenome coordinate JSON file (OUTPUT) |
Example | structural_pangenome build-coordinate deltas/pangenome__fasta_vs_assembly_1_bbmhFilter.delta o outputs/coordinate_json.json --pretty --unzipped -m |
| haptic example | haptic build-json deltas/pangenome__fasta_vs_assembly_1_bbmhFilter.delta -o outputs/coordinate-json.json |
| Usage | structural_pangenome build-coordinate [-h] (-p PREFIX | -o OUTPUT) [–unzipped] [--pretty] [-m [METRICS]] DELTA [DELTA ...] |
Can be Parallelized | Yes |
Optional | No |
...
Description | Get the sequence length distribution of the pangenome segment with coordinate in the pangenome |
Command | structural_pangenome find-coordinate-seqlen pangenome_coordinate_file sequence_lengths_file -o output_file -g OR structural_pangenome find-coordinate-seqlen pangenome_coordinate_file sequence_lengths_file -p prefix_folder -g |
| haptic command | haptic find-seqlen reverse_filtered_delta_file -o output_file -g OR haptic find-seqlen reverse_filtered_delta_file -p prefix_folder -g |
Parameters | o: output filename (with complete path) p: prefix_folder which stores the resulting output file (with complete path) g: optional, apply to yield generate sequence length distribution graph |
Input | pangenome coordinate file (COORDINATE) - From Step8. sequence lengths file (.csv) (SEQLEN) - From Step2.4 |
output | pangenome_coordinate_seqLength Graph (OUTPUT) |
| Usage | structural_pangenome find-coordinate-seqlen [-h] (-p PREFIX | -o OUTPUT) [-g] COORDINATE SEQLEN |
Example | structural_pangenome find-coordinate-seqlen Step8.CoordPangenome/coordAssem_pangenome.json Step2.4.seqLens/pangenome__fasta_seqlen.csv -p outputs/seqlenPangenome -g |
| haptic example | haptic find-seqlen deltas/pangenome__fasta_vs_assembly_1_bbmhFiter.delta -p outputs/seqlen |
Can be Parallelized | Yes |
Optional | Yes |
...
| Description | Builds a pangenome path json file, based on the coordinate json file |
| Command | structural_pangenome build-path pangenome_coordinate_json_file -o output file |
| Parameters | o: output filename (with complete path) p: prefix_folder which stores the resulting output file (with complete path) unzipped, optional: set this flag to generated an uncompressed file (–unzipped) pretty, optional: set this flag to generated a json file that is human readable (–pretty) |
| Input | pangenome coordinate JSON file (JSON) - From Step8. |
| output | pangenome path JSON FILE (OUTPUT) |
| Usage | structural_pangenome build-path [-h] (-p PREFIX | -o OUTPUT) [–unzipped] [–pretty] JSON |
| Example | structural_pangenome build-path Step8.CoordPangenome/coordAssem_pangenome.json -o 10.PathPangenome/path__pangenome.json --unzipped --pretty |
| Can be Parallelized | Yes |
| Optional | No |
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