GenoChar 0.6.3.2__tar.gz

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  1. genochar-0.6.3.2/GenoChar.egg-info/PKG-INFO +296 -0
  2. genochar-0.6.3.2/GenoChar.egg-info/SOURCES.txt +19 -0
  3. genochar-0.6.3.2/GenoChar.egg-info/dependency_links.txt +1 -0
  4. genochar-0.6.3.2/GenoChar.egg-info/entry_points.txt +2 -0
  5. genochar-0.6.3.2/GenoChar.egg-info/requires.txt +2 -0
  6. genochar-0.6.3.2/GenoChar.egg-info/top_level.txt +1 -0
  7. genochar-0.6.3.2/LICENSE +21 -0
  8. genochar-0.6.3.2/PKG-INFO +296 -0
  9. genochar-0.6.3.2/README.md +280 -0
  10. genochar-0.6.3.2/genochar/__init__.py +2 -0
  11. genochar-0.6.3.2/genochar/assembly_stats.py +124 -0
  12. genochar-0.6.3.2/genochar/checkm2.py +35 -0
  13. genochar-0.6.3.2/genochar/cli.py +585 -0
  14. genochar-0.6.3.2/genochar/coverage.py +48 -0
  15. genochar-0.6.3.2/genochar/gff_stats.py +223 -0
  16. genochar-0.6.3.2/genochar/managed_envs.py +201 -0
  17. genochar-0.6.3.2/genochar/metadata.py +47 -0
  18. genochar-0.6.3.2/genochar/pipeline.py +172 -0
  19. genochar-0.6.3.2/genochar/utils.py +228 -0
  20. genochar-0.6.3.2/pyproject.toml +40 -0
  21. genochar-0.6.3.2/setup.cfg +4 -0
genochar-0.6.3.2/GenoChar.egg-info/PKG-INFO ADDED
@@ -0,0 +1,296 @@
1
+ Metadata-Version: 2.4
2
+ Name: GenoChar
3
+ Version: 0.6.3.2
4
+ Summary: GenoChar: summarize-first genome characterization workflow with one-time managed setup for Prokka and CheckM2
5
+ Author: Jun Won Lee
6
+ License-Expression: MIT
7
+ Project-URL: Homepage, https://github.com/ljunwon1114/GenoChar
8
+ Project-URL: Issues, https://github.com/ljunwon1114/GenoChar/issues
9
+ Keywords: bioinformatics,genomics,genome-assembly,genome-annotation,microbiology,bacteria,archaea,checkm2,prokka
10
+ Requires-Python: >=3.10
11
+ Description-Content-Type: text/markdown
12
+ License-File: LICENSE
13
+ Requires-Dist: pandas>=2.0
14
+ Requires-Dist: openpyxl>=3.1
15
+ Dynamic: license-file
16
+
17
+ # GenoChar
18
+
19
+ **GenoChar** generates publication-ready genome characterization tables for bacterial and archaeal genomes.
20
+
21
+ Version **0.6.3.2** keeps the **single-command, summarize-first interface**, but adds a practical solution for external-tool dependency conflicts:
22
+
23
+ - **`genochar`** builds the final genome characterization table
24
+ - **`genochar setup`** prepares **managed Prokka and CheckM2 conda environments** under `~/.genochar`
25
+ - later, a normal `genochar ... --check --annotate prokka` run automatically calls those managed environments with `conda run -p ...`
26
+
27
+ That means users do **not** need to manually solve a shared Prokka/CheckM2 environment.
28
+
29
+ The main output is a wide table with one row per strain. Optional outputs include a feature-style table and an Excel workbook.
30
+
31
+ **Naming note:** the project/display name is **GenoChar**, while the Python package name and command-line executable remain lowercase as `genochar`.
32
+
33
+ ## What the tool computes
34
+
35
+ ### FASTA-derived fields
36
+ These work even if you provide only FASTA files:
37
+
38
+ - `Strain`
39
+ - `Strain name`
40
+ - `Genus`
41
+ - `Species`
42
+ - `Accession`
43
+ - `Genome size (bp)`
44
+ - `GC content (%)`
45
+ - `No. of contigs`
46
+ - `N50 (bp)`
47
+ - `N90 (bp)`
48
+ - `L50`
49
+ - `L90`
50
+ - `Longest contig (bp)`
51
+ - `Gaps (N per 100 kb)`
52
+
53
+ ### GFF-derived fields
54
+ These are added when you provide GFF files or ask GenoChar to create annotation files:
55
+
56
+ - `CDSs`
57
+ - `tRNAs`
58
+ - `rRNAs`
59
+ - `tmRNA`
60
+ - `misc RNA`
61
+ - `Repeat regions`
62
+ - `16S rRNA count`
63
+ - `16S rRNA length (bp)`
64
+ - `16S rRNA contig`
65
+ - `16S rRNA sequence`
66
+
67
+ ### CheckM2-derived fields
68
+ These are added when you provide or generate a CheckM2 report:
69
+
70
+ - `Completeness (%)`
71
+ - `Contamination (%)`
72
+
73
+ ### User-supplied metadata
74
+ Optional input tables can add:
75
+
76
+ - `Sequencing coverage (×)`
77
+ - `Sequencing platforms`
78
+ - `Assembly method`
79
+ - `Genus`
80
+ - `Species`
81
+ - `Accession`
82
+ - `Repeat regions`
83
+
84
+ ## Default output columns
85
+
86
+ The main output table contains:
87
+
88
+ - `Strain`
89
+ - `Strain name`
90
+ - `Genus`
91
+ - `Species`
92
+ - `Accession`
93
+ - `Genome size (bp)`
94
+ - `GC content (%)`
95
+ - `No. of contigs`
96
+ - `N50 (bp)`
97
+ - `N90 (bp)`
98
+ - `L50`
99
+ - `L90`
100
+ - `Longest contig (bp)`
101
+ - `Gaps (N per 100 kb)`
102
+ - `Sequencing coverage (×)`
103
+ - `Sequencing platforms`
104
+ - `Assembly method`
105
+ - `CDSs`
106
+ - `tRNAs`
107
+ - `rRNAs`
108
+ - `tmRNA`
109
+ - `misc RNA`
110
+ - `Repeat regions`
111
+ - `16S rRNA count`
112
+ - `16S rRNA length (bp)`
113
+ - `16S rRNA contig`
114
+ - `16S rRNA sequence`
115
+ - `Completeness (%)`
116
+ - `Contamination (%)`
117
+
118
+ ## Installation
119
+
120
+ Clone the repository and install GenoChar into the active Python environment:
121
+
122
+ ```bash
123
+ git clone https://github.com/ljunwon1114/GenoChar.git
124
+ cd GenoChar
125
+ pip install -e .
126
+ ```
127
+
128
+ If you just want the latest GitHub version without cloning for development, you can also use:
129
+
130
+ ```bash
131
+ pip install git+https://github.com/ljunwon1114/GenoChar.git
132
+ ```
133
+
134
+ ### Core Python requirement
135
+
136
+ GenoChar itself is lightweight. The **core package** now declares:
137
+
138
+ - `requires-python >=3.10`
139
+
140
+ The external tools are the difficult part, so v0.6.3.2 no longer assumes that Prokka and CheckM2 should share the same environment.
141
+
142
+ ## One-time managed setup (recommended)
143
+
144
+ Run this once:
145
+
146
+ ```bash
147
+ genochar setup
148
+ ```
149
+
150
+ This creates managed environments under `~/.genochar`, typically:
151
+
152
+ ```text
153
+ ~/.genochar/
154
+ config.json
155
+ envs/
156
+ prokka/
157
+ checkm2/
158
+ databases/
159
+ CheckM2_database/
160
+ ```
161
+
162
+ After that, normal workflow commands automatically use those managed environments when `--annotate prokka` and/or `--check` are requested.
163
+
164
+ When `--check` is used, GenoChar now passes the resolved input FASTA files directly to `checkm2 predict --input ...`, matching the official CheckM2 interface that accepts either a folder of bins or a list of FASTA files.
165
+
166
+ ### Reuse an existing CheckM2 database
167
+
168
+ If you already downloaded the CheckM2 database, point setup at it directly:
169
+
170
+ ```bash
171
+ genochar setup --checkm2-db /home/jwlee/databases/CheckM2_database/uniref100.KO.1.dmnd
172
+ ```
173
+
174
+ You can also pass a directory that contains the `.dmnd` file.
175
+
176
+ ### Optional setup flags
177
+
178
+ ```bash
179
+ genochar setup --skip-prokka
180
+ genochar setup --skip-checkm2
181
+ genochar setup --force
182
+ ```
183
+
184
+ - `--skip-prokka`: only prepare CheckM2
185
+ - `--skip-checkm2`: only prepare Prokka
186
+ - `--force`: recreate managed environments even if they already exist
187
+
188
+ ## Command overview
189
+
190
+ ### A. FASTA only
191
+
192
+ ```bash
193
+ genochar -i "assemblies/*.fasta" -o genome_characterization.tsv
194
+ ```
195
+
196
+ ### B. FASTA + existing GFF + existing CheckM2 report
197
+
198
+ ```bash
199
+ genochar -i "assemblies/*.fasta" --gff "annotations/*.gff*" --check-report checkm2_out/quality_report.tsv -o genome_characterization.tsv
200
+ ```
201
+
202
+ ### C. FASTA + managed CheckM2 first + managed Prokka annotation
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+
204
+ ```bash
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+ genochar -i "assemblies/*.fasta" --check --annotate prokka -k Archaea -t 8 -w genochar_work -o genome_characterization.tsv
206
+ ```
207
+
208
+ ### D. Reuse existing GFF files automatically
209
+
210
+ ```bash
211
+ genochar -i "assemblies/*.fasta" --annotate existing --check-report checkm2_out/quality_report.tsv -o genome_characterization.tsv
212
+ ```
213
+
214
+ ### E. Reuse explicitly supplied GFF files in existing-annotation mode
215
+
216
+ ```bash
217
+ genochar -i "assemblies/*.fasta" --annotate existing --gff "annotations/*.gff*" --check-report checkm2_out/quality_report.tsv -o genome_characterization.tsv
218
+ ```
219
+
220
+ ## Optional extra outputs
221
+
222
+ ### Feature-style table
223
+
224
+ ```bash
225
+ genochar -i "assemblies/*.fasta" -f genome_characterization_feature.tsv -o genome_characterization.tsv
226
+ ```
227
+
228
+ ### Excel workbook
229
+
230
+ ```bash
231
+ genochar -i "assemblies/*.fasta" -x genome_characterization.xlsx -o genome_characterization.tsv
232
+ ```
233
+
234
+ ## Coverage input
235
+
236
+ Coverage cannot be derived from FASTA alone. If you want to fill `Sequencing coverage (×)`, provide a coverage table.
237
+
238
+ Example:
239
+
240
+ ```text
241
+ Strain Coverage
242
+ IOH03 55.7
243
+ IOH05 50.3
244
+ ```
245
+
246
+ or
247
+
248
+ ```text
249
+ Strain Total bases
250
+ IOH03 110.8 Mbp
251
+ IOH05 107.6 Mbp
252
+ ```
253
+
254
+ If `Total bases` is provided, GenoChar computes:
255
+
256
+ ```text
257
+ Sequencing coverage (×) = Total bases / Genome size
258
+ ```
259
+
260
+ ## Metadata input
261
+
262
+ Optional metadata columns include:
263
+
264
+ - `Strain`
265
+ - `Sequencing platforms`
266
+ - `Assembly method`
267
+ - `Genus`
268
+ - `Species`
269
+ - `Accession`
270
+ - `Repeat regions`
271
+ - `Sequencing coverage (×)`
272
+
273
+ Example:
274
+
275
+ ```text
276
+ Strain Genus Species Accession Sequencing platforms Assembly method
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+ IOH03 Thermococcus waiotapuensis GCF_032304395 Illumina iSeq 100 Unicycler (short-read assembly)
278
+ IOH05 Thermococcus sp. GCA_000000000 Illumina iSeq 100 Unicycler (short-read assembly)
279
+ ```
280
+
281
+ ## Notes
282
+
283
+ - **GenoChar** is summarize-first by default. If you only pass FASTA, GFF, CheckM2, coverage, and metadata inputs, it behaves like a direct summarization tool.
284
+ - **`genochar setup`** is the recommended way to prepare Prokka and CheckM2 without forcing them into one shared environment.
285
+ - `--annotate prokka` tells GenoChar to create annotation files before building the final table.
286
+ - `--annotate existing` tells GenoChar to reuse nearby GFF files or explicitly supplied `--gff` inputs.
287
+ - `--check` runs CheckM2 internally **before annotation** and automatically integrates the resulting `quality_report.tsv` into the final table.
288
+ - `--check-report` reuses an existing CheckM2 `quality_report.tsv` file.
289
+ - `--check` and `--check-report` are mutually exclusive.
290
+ - `--gff` is intended for existing annotation files and should not be combined with `--annotate prokka`.
291
+ - If more than one 16S rRNA feature is found, GenoChar stores the longest 16S sequence in the main table.
292
+ - Legacy `genochar summarize ...` and `genochar pipeline ...` calls are still accepted in v0.6.3, but the preferred interface is the single-command form shown above.
293
+
294
+ ## License
295
+
296
+ MIT
genochar-0.6.3.2/GenoChar.egg-info/SOURCES.txt ADDED
@@ -0,0 +1,19 @@
1
+ LICENSE
2
+ README.md
3
+ pyproject.toml
4
+ GenoChar.egg-info/PKG-INFO
5
+ GenoChar.egg-info/SOURCES.txt
6
+ GenoChar.egg-info/dependency_links.txt
7
+ GenoChar.egg-info/entry_points.txt
8
+ GenoChar.egg-info/requires.txt
9
+ GenoChar.egg-info/top_level.txt
10
+ genochar/__init__.py
11
+ genochar/assembly_stats.py
12
+ genochar/checkm2.py
13
+ genochar/cli.py
14
+ genochar/coverage.py
15
+ genochar/gff_stats.py
16
+ genochar/managed_envs.py
17
+ genochar/metadata.py
18
+ genochar/pipeline.py
19
+ genochar/utils.py
genochar-0.6.3.2/GenoChar.egg-info/entry_points.txt ADDED
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1
+ [console_scripts]
2
+ genochar = genochar.cli:main
genochar-0.6.3.2/GenoChar.egg-info/requires.txt ADDED
@@ -0,0 +1,2 @@
1
+ pandas>=2.0
2
+ openpyxl>=3.1
genochar-0.6.3.2/GenoChar.egg-info/top_level.txt ADDED
@@ -0,0 +1 @@
1
+ genochar
genochar-0.6.3.2/LICENSE ADDED
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1
+ MIT License
2
+
3
+ Copyright (c) 2026 Jun Won Lee
4
+
5
+ Permission is hereby granted, free of charge, to any person obtaining a copy
6
+ of this software and associated documentation files (the "Software"), to deal
7
+ in the Software without restriction, including without limitation the rights
8
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9
+ copies of the Software, and to permit persons to whom the Software is
10
+ furnished to do so, subject to the following conditions:
11
+
12
+ The above copyright notice and this permission notice shall be included in all
13
+ copies or substantial portions of the Software.
14
+
15
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21
+ SOFTWARE.
genochar-0.6.3.2/PKG-INFO ADDED
@@ -0,0 +1,296 @@
1
+ Metadata-Version: 2.4
2
+ Name: GenoChar
3
+ Version: 0.6.3.2
4
+ Summary: GenoChar: summarize-first genome characterization workflow with one-time managed setup for Prokka and CheckM2
5
+ Author: Jun Won Lee
6
+ License-Expression: MIT
7
+ Project-URL: Homepage, https://github.com/ljunwon1114/GenoChar
8
+ Project-URL: Issues, https://github.com/ljunwon1114/GenoChar/issues
9
+ Keywords: bioinformatics,genomics,genome-assembly,genome-annotation,microbiology,bacteria,archaea,checkm2,prokka
10
+ Requires-Python: >=3.10
11
+ Description-Content-Type: text/markdown
12
+ License-File: LICENSE
13
+ Requires-Dist: pandas>=2.0
14
+ Requires-Dist: openpyxl>=3.1
15
+ Dynamic: license-file
16
+
17
+ # GenoChar
18
+
19
+ **GenoChar** generates publication-ready genome characterization tables for bacterial and archaeal genomes.
20
+
21
+ Version **0.6.3.2** keeps the **single-command, summarize-first interface**, but adds a practical solution for external-tool dependency conflicts:
22
+
23
+ - **`genochar`** builds the final genome characterization table
24
+ - **`genochar setup`** prepares **managed Prokka and CheckM2 conda environments** under `~/.genochar`
25
+ - later, a normal `genochar ... --check --annotate prokka` run automatically calls those managed environments with `conda run -p ...`
26
+
27
+ That means users do **not** need to manually solve a shared Prokka/CheckM2 environment.
28
+
29
+ The main output is a wide table with one row per strain. Optional outputs include a feature-style table and an Excel workbook.
30
+
31
+ **Naming note:** the project/display name is **GenoChar**, while the Python package name and command-line executable remain lowercase as `genochar`.
32
+
33
+ ## What the tool computes
34
+
35
+ ### FASTA-derived fields
36
+ These work even if you provide only FASTA files:
37
+
38
+ - `Strain`
39
+ - `Strain name`
40
+ - `Genus`
41
+ - `Species`
42
+ - `Accession`
43
+ - `Genome size (bp)`
44
+ - `GC content (%)`
45
+ - `No. of contigs`
46
+ - `N50 (bp)`
47
+ - `N90 (bp)`
48
+ - `L50`
49
+ - `L90`
50
+ - `Longest contig (bp)`
51
+ - `Gaps (N per 100 kb)`
52
+
53
+ ### GFF-derived fields
54
+ These are added when you provide GFF files or ask GenoChar to create annotation files:
55
+
56
+ - `CDSs`
57
+ - `tRNAs`
58
+ - `rRNAs`
59
+ - `tmRNA`
60
+ - `misc RNA`
61
+ - `Repeat regions`
62
+ - `16S rRNA count`
63
+ - `16S rRNA length (bp)`
64
+ - `16S rRNA contig`
65
+ - `16S rRNA sequence`
66
+
67
+ ### CheckM2-derived fields
68
+ These are added when you provide or generate a CheckM2 report:
69
+
70
+ - `Completeness (%)`
71
+ - `Contamination (%)`
72
+
73
+ ### User-supplied metadata
74
+ Optional input tables can add:
75
+
76
+ - `Sequencing coverage (×)`
77
+ - `Sequencing platforms`
78
+ - `Assembly method`
79
+ - `Genus`
80
+ - `Species`
81
+ - `Accession`
82
+ - `Repeat regions`
83
+
84
+ ## Default output columns
85
+
86
+ The main output table contains:
87
+
88
+ - `Strain`
89
+ - `Strain name`
90
+ - `Genus`
91
+ - `Species`
92
+ - `Accession`
93
+ - `Genome size (bp)`
94
+ - `GC content (%)`
95
+ - `No. of contigs`
96
+ - `N50 (bp)`
97
+ - `N90 (bp)`
98
+ - `L50`
99
+ - `L90`
100
+ - `Longest contig (bp)`
101
+ - `Gaps (N per 100 kb)`
102
+ - `Sequencing coverage (×)`
103
+ - `Sequencing platforms`
104
+ - `Assembly method`
105
+ - `CDSs`
106
+ - `tRNAs`
107
+ - `rRNAs`
108
+ - `tmRNA`
109
+ - `misc RNA`
110
+ - `Repeat regions`
111
+ - `16S rRNA count`
112
+ - `16S rRNA length (bp)`
113
+ - `16S rRNA contig`
114
+ - `16S rRNA sequence`
115
+ - `Completeness (%)`
116
+ - `Contamination (%)`
117
+
118
+ ## Installation
119
+
120
+ Clone the repository and install GenoChar into the active Python environment:
121
+
122
+ ```bash
123
+ git clone https://github.com/ljunwon1114/GenoChar.git
124
+ cd GenoChar
125
+ pip install -e .
126
+ ```
127
+
128
+ If you just want the latest GitHub version without cloning for development, you can also use:
129
+
130
+ ```bash
131
+ pip install git+https://github.com/ljunwon1114/GenoChar.git
132
+ ```
133
+
134
+ ### Core Python requirement
135
+
136
+ GenoChar itself is lightweight. The **core package** now declares:
137
+
138
+ - `requires-python >=3.10`
139
+
140
+ The external tools are the difficult part, so v0.6.3.2 no longer assumes that Prokka and CheckM2 should share the same environment.
141
+
142
+ ## One-time managed setup (recommended)
143
+
144
+ Run this once:
145
+
146
+ ```bash
147
+ genochar setup
148
+ ```
149
+
150
+ This creates managed environments under `~/.genochar`, typically:
151
+
152
+ ```text
153
+ ~/.genochar/
154
+ config.json
155
+ envs/
156
+ prokka/
157
+ checkm2/
158
+ databases/
159
+ CheckM2_database/
160
+ ```
161
+
162
+ After that, normal workflow commands automatically use those managed environments when `--annotate prokka` and/or `--check` are requested.
163
+
164
+ When `--check` is used, GenoChar now passes the resolved input FASTA files directly to `checkm2 predict --input ...`, matching the official CheckM2 interface that accepts either a folder of bins or a list of FASTA files.
165
+
166
+ ### Reuse an existing CheckM2 database
167
+
168
+ If you already downloaded the CheckM2 database, point setup at it directly:
169
+
170
+ ```bash
171
+ genochar setup --checkm2-db /home/jwlee/databases/CheckM2_database/uniref100.KO.1.dmnd
172
+ ```
173
+
174
+ You can also pass a directory that contains the `.dmnd` file.
175
+
176
+ ### Optional setup flags
177
+
178
+ ```bash
179
+ genochar setup --skip-prokka
180
+ genochar setup --skip-checkm2
181
+ genochar setup --force
182
+ ```
183
+
184
+ - `--skip-prokka`: only prepare CheckM2
185
+ - `--skip-checkm2`: only prepare Prokka
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+ - `--force`: recreate managed environments even if they already exist
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+
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+ ## Command overview
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+
190
+ ### A. FASTA only
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+
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+ ```bash
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+ genochar -i "assemblies/*.fasta" -o genome_characterization.tsv
194
+ ```
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+
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+ ### B. FASTA + existing GFF + existing CheckM2 report
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+
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+ ```bash
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+ genochar -i "assemblies/*.fasta" --gff "annotations/*.gff*" --check-report checkm2_out/quality_report.tsv -o genome_characterization.tsv
200
+ ```
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+
202
+ ### C. FASTA + managed CheckM2 first + managed Prokka annotation
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+
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+ ```bash
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+ genochar -i "assemblies/*.fasta" --check --annotate prokka -k Archaea -t 8 -w genochar_work -o genome_characterization.tsv
206
+ ```
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+
208
+ ### D. Reuse existing GFF files automatically
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+
210
+ ```bash
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+ genochar -i "assemblies/*.fasta" --annotate existing --check-report checkm2_out/quality_report.tsv -o genome_characterization.tsv
212
+ ```
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+
214
+ ### E. Reuse explicitly supplied GFF files in existing-annotation mode
215
+
216
+ ```bash
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+ genochar -i "assemblies/*.fasta" --annotate existing --gff "annotations/*.gff*" --check-report checkm2_out/quality_report.tsv -o genome_characterization.tsv
218
+ ```
219
+
220
+ ## Optional extra outputs
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+
222
+ ### Feature-style table
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+
224
+ ```bash
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+ genochar -i "assemblies/*.fasta" -f genome_characterization_feature.tsv -o genome_characterization.tsv
226
+ ```
227
+
228
+ ### Excel workbook
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+
230
+ ```bash
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+ genochar -i "assemblies/*.fasta" -x genome_characterization.xlsx -o genome_characterization.tsv
232
+ ```
233
+
234
+ ## Coverage input
235
+
236
+ Coverage cannot be derived from FASTA alone. If you want to fill `Sequencing coverage (×)`, provide a coverage table.
237
+
238
+ Example:
239
+
240
+ ```text
241
+ Strain Coverage
242
+ IOH03 55.7
243
+ IOH05 50.3
244
+ ```
245
+
246
+ or
247
+
248
+ ```text
249
+ Strain Total bases
250
+ IOH03 110.8 Mbp
251
+ IOH05 107.6 Mbp
252
+ ```
253
+
254
+ If `Total bases` is provided, GenoChar computes:
255
+
256
+ ```text
257
+ Sequencing coverage (×) = Total bases / Genome size
258
+ ```
259
+
260
+ ## Metadata input
261
+
262
+ Optional metadata columns include:
263
+
264
+ - `Strain`
265
+ - `Sequencing platforms`
266
+ - `Assembly method`
267
+ - `Genus`
268
+ - `Species`
269
+ - `Accession`
270
+ - `Repeat regions`
271
+ - `Sequencing coverage (×)`
272
+
273
+ Example:
274
+
275
+ ```text
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+ Strain Genus Species Accession Sequencing platforms Assembly method
277
+ IOH03 Thermococcus waiotapuensis GCF_032304395 Illumina iSeq 100 Unicycler (short-read assembly)
278
+ IOH05 Thermococcus sp. GCA_000000000 Illumina iSeq 100 Unicycler (short-read assembly)
279
+ ```
280
+
281
+ ## Notes
282
+
283
+ - **GenoChar** is summarize-first by default. If you only pass FASTA, GFF, CheckM2, coverage, and metadata inputs, it behaves like a direct summarization tool.
284
+ - **`genochar setup`** is the recommended way to prepare Prokka and CheckM2 without forcing them into one shared environment.
285
+ - `--annotate prokka` tells GenoChar to create annotation files before building the final table.
286
+ - `--annotate existing` tells GenoChar to reuse nearby GFF files or explicitly supplied `--gff` inputs.
287
+ - `--check` runs CheckM2 internally **before annotation** and automatically integrates the resulting `quality_report.tsv` into the final table.
288
+ - `--check-report` reuses an existing CheckM2 `quality_report.tsv` file.
289
+ - `--check` and `--check-report` are mutually exclusive.
290
+ - `--gff` is intended for existing annotation files and should not be combined with `--annotate prokka`.
291
+ - If more than one 16S rRNA feature is found, GenoChar stores the longest 16S sequence in the main table.
292
+ - Legacy `genochar summarize ...` and `genochar pipeline ...` calls are still accepted in v0.6.3, but the preferred interface is the single-command form shown above.
293
+
294
+ ## License
295
+
296
+ MIT