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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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Fix snakemake version to be less than 8.6.0 to fix temp delete issue.
#216
LeeBergstrand
closed
2 days ago
0
downgrade to freebayes 1.3.6 to be compatible with pypolca install.
#215
LeeBergstrand
closed
4 days ago
0
Merge develop_lee into develop
#214
LeeBergstrand
opened
6 days ago
0
Add code for aggregating checkm stats across all samples into a singl…
#213
LeeBergstrand
closed
6 days ago
0
Aggregate CheckM stats into single report
#212
LeeBergstrand
closed
6 days ago
0
Aggregate CheckM stats across all samples into one report
#211
LeeBergstrand
closed
1 week ago
0
simplify label further
#210
LeeBergstrand
closed
1 week ago
0
We only need one label
#209
LeeBergstrand
closed
1 week ago
0
remove post end-repair assemblies as they are almost always identical…
#208
LeeBergstrand
closed
1 week ago
0
simplify assembly QUAST outputs.
#207
LeeBergstrand
closed
6 days ago
0
A -p meta to the contig start gene prediction to handle small circula…
#206
LeeBergstrand
closed
1 week ago
0
A -p meta to the contig start search to handle small circular contigs.
#205
LeeBergstrand
closed
6 days ago
2
refactor qc functions allow the code to work with total bases values …
#204
LeeBergstrand
closed
2 weeks ago
0
raise value error if no contigs pass coverage filter.
#203
LeeBergstrand
closed
2 weeks ago
0
Question about QC filtering
#202
LeeBergstrand
closed
6 days ago
3
Qc before after comparison allow kbp gbp values in Total Bases Column
#201
LeeBergstrand
closed
6 days ago
0
raise value error if no contigs pass coverage filter.
#200
LeeBergstrand
closed
6 days ago
1
Rotary Hangs When No Contigs Pass Coverage Filter
#199
LeeBergstrand
opened
3 weeks ago
1
Merge pull request #194 from rotary-genomics/fix_circularize_missing_…
#198
LeeBergstrand
closed
1 month ago
0
Merge branch 'develop' into aggregate_stats
#197
LeeBergstrand
closed
1 month ago
0
Manually write the contigs file that is missing.
#196
LeeBergstrand
closed
1 month ago
0
Develop
#195
LeeBergstrand
closed
1 month ago
0
Fix circularize medaka missing contigs file
#194
LeeBergstrand
closed
1 month ago
1
Rotary fails to repolish circular contigs due to workflow errors.
#193
LeeBergstrand
closed
1 month ago
15
Aggregate Assembly Stats Across Samples
#192
LeeBergstrand
closed
1 month ago
0
Aggregate quast stats
#191
LeeBergstrand
closed
1 month ago
0
Aggregate Assembly Stats Across Samples
#190
LeeBergstrand
closed
1 month ago
0
Aggregate stats
#189
LeeBergstrand
closed
1 month ago
0
Snakemake 8
#188
LeeBergstrand
closed
1 month ago
0
Aggregate QC Stats Across Samples
#187
LeeBergstrand
closed
6 days ago
2
Snakemake 8
#186
LeeBergstrand
closed
1 month 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
1 month 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
1 month 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
2 months ago
0
Improve qc stats
#171
LeeBergstrand
closed
2 months ago
0
add missing unzip to download environment.
#170
LeeBergstrand
closed
2 months ago
0
add missing unzip to download environment.
#169
LeeBergstrand
closed
2 months ago
0
Update improve qc stats
#168
LeeBergstrand
closed
2 months ago
0
Delete Unused Branches
#167
LeeBergstrand
closed
2 months ago
4
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