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rotary-genomics
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rotary
Assembly/annotation workflow for Nanopore-based microbial genome data containing circular DNA elements
BSD 3-Clause "New" or "Revised" License
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Qc before after comparison allow kbp gbp values in Total Bases Column
#201
LeeBergstrand
opened
1 day ago
0
raise value error if no contigs pass coverage filter.
#200
LeeBergstrand
opened
3 days ago
1
Rotary Hangs When No Contigs Pass Coverage Filter
#199
LeeBergstrand
opened
3 days ago
1
Merge pull request #194 from rotary-genomics/fix_circularize_missing_…
#198
LeeBergstrand
closed
1 week ago
0
Merge branch 'develop' into aggregate_stats
#197
LeeBergstrand
closed
2 weeks ago
0
Manually write the contigs file that is missing.
#196
LeeBergstrand
closed
2 weeks ago
0
Develop
#195
LeeBergstrand
closed
2 weeks ago
0
Fix circularize medaka missing contigs file
#194
LeeBergstrand
closed
1 week ago
1
Rotary fails to repolish circular contigs due to workflow errors.
#193
LeeBergstrand
closed
1 week ago
15
Aggregate Assembly Stats Across Samples
#192
LeeBergstrand
closed
2 weeks ago
0
Aggregate quast stats
#191
LeeBergstrand
closed
3 weeks ago
0
Aggregate Assembly Stats Across Samples
#190
LeeBergstrand
closed
3 weeks ago
0
Aggregate stats
#189
LeeBergstrand
closed
3 weeks ago
0
Snakemake 8
#188
LeeBergstrand
closed
3 weeks ago
0
Aggregate QC Stats Across Samples
#187
LeeBergstrand
opened
3 weeks ago
2
Snakemake 8
#186
LeeBergstrand
closed
2 weeks ago
1
Add download command
#185
LeeBergstrand
closed
1 month ago
0
Add download command
#184
LeeBergstrand
closed
1 month ago
0
Refactor quality report generation
#183
LeeBergstrand
closed
1 month ago
0
Readme Demo Data Download Fails
#182
LeeBergstrand
opened
1 month ago
1
Refactor quality report generation to use wildcards
#181
LeeBergstrand
closed
2 weeks ago
6
Merge pull request #177 from rotary-genomics/change_gtdb_url
#180
LeeBergstrand
closed
1 month ago
0
Improve qc stats
#179
LeeBergstrand
closed
1 month ago
0
Revert "Add assembly stats"
#178
LeeBergstrand
closed
1 month ago
0
update the GTDB url to point to the mirror site rather than the prima…
#177
LeeBergstrand
closed
1 month ago
0
Move to less threads per sample for multi-sample runs.
#176
LeeBergstrand
opened
1 month ago
6
Add download command
#175
LeeBergstrand
closed
2 weeks ago
4
Change GTDB URL to use mirror site for much faster database downloads.
#174
LeeBergstrand
closed
1 month ago
1
Add assembly stats
#173
LeeBergstrand
closed
1 month ago
2
Merge pull request #171 from rotary-genomics/improve_qc_stats
#172
LeeBergstrand
closed
1 month ago
0
Improve qc stats
#171
LeeBergstrand
closed
1 month ago
0
add missing unzip to download environment.
#170
LeeBergstrand
closed
1 month ago
0
add missing unzip to download environment.
#169
LeeBergstrand
closed
1 month ago
0
Update improve qc stats
#168
LeeBergstrand
closed
1 month ago
0
Delete Unused Branches
#167
LeeBergstrand
closed
1 month ago
4
Add Checkm2 db version to Checkm2 database
#166
LeeBergstrand
opened
1 month ago
0
Specify CheckM2 DB path
#165
jmtsuji
closed
1 month ago
3
DB error for CheckM2
#164
jmtsuji
closed
1 month ago
6
Install pungi and spokewrench via conda YAML files
#163
jmtsuji
closed
1 month ago
3
Upgrade to GTDB r220 and GTDB-Tk v2.4.0
#162
jmtsuji
closed
1 month ago
3
Add QC Stats
#161
LeeBergstrand
closed
1 month ago
9
Metagenomics Mode (MetaFlye and Binning)
#160
LeeBergstrand
opened
2 months ago
5
Add option for nano-corr in flye / repair script
#159
LeeBergstrand
closed
2 months ago
2
Make symlinks of the QC'ed short read at the start to simplify logging
#158
LeeBergstrand
closed
2 months ago
2
Improve run reports for rotary
#157
LeeBergstrand
opened
2 months ago
6
Address TODOs in the Snakefiles
#156
LeeBergstrand
opened
2 months ago
0
Allow annotation steps to be be turned on and off in config.
#154
LeeBergstrand
closed
2 months ago
1
add code to allow medaka to automatically detect base caller model.
#153
LeeBergstrand
closed
2 months ago
1
Separate utilities into spokewrench
#152
jmtsuji
closed
1 month ago
9
Improve Documentation For aggregate_contigs in circularize.smk
#151
LeeBergstrand
opened
2 months ago
0
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