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Support for more minimap2 arguments (added since v2.22) #37

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Dec 13, 2024
Merged

Support for more minimap2 arguments (added since v2.22) #37

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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -88,7 +88,7 @@ Each step of the installation process is expected to take a matter of seconds.

| Command | Default | Description |
| :------- | :----- | :-------- |
|--type | map-ont | denote sequencer [short-read:sr, Pac-Bio:map-pb, ONT:map-ont] |
|--type | map-ont | denote sequencer [short-read:sr, Pac-Bio:map-pb, ONT:map-ont, Nanopore Q20:lr:hq, PacBio HiFi:map-hifi, traditional cDNA:splice:hq] |
|--min-abundance| 0.0001| generates results with species relative abundance above this value in addition to full results; .01 = 1%|
|--db| $EMU_DATABASE_DIR| path to emu database; directory must include the following files: names_df.tsv, nodes_df.tsv, species_taxid.fasta, unqiue_taxids.tsv|
|--N| 50| max number of alignments utilized for each read in minimap2|
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4 changes: 2 additions & 2 deletions emu
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Expand Up @@ -697,8 +697,8 @@ if __name__ == "__main__":
'input_file', type=str, nargs='+',
help='filepath to input nt sequence file')
abundance_parser.add_argument(
'--type', '-x', choices=['map-ont', 'map-pb', 'sr'], default='map-ont',
help='short-read: sr, Pac-Bio:map-pb, ONT:map-ont [map-ont]')
'--type', '-x', choices=['map-ont', 'map-pb', 'sr', 'lr:hq', 'map-hifi', 'splice:hq'], default='map-ont',
help='short-read: sr, Pac-Bio:map-pb, ONT:map-ont, ... [map-ont]')
abundance_parser.add_argument(
'--min-abundance', '-a', type=float, default=0.0001,
help='min species abundance in results [0.0001]')
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2 changes: 1 addition & 1 deletion environment.yml
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Expand Up @@ -11,4 +11,4 @@ dependencies:
- numpy >=1.11
- pandas >=1.1
- flatten-dict
- minimap2 >=2.22
- minimap2 >=2.27