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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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Refactor sample
#115
LeeBergstrand
closed
5 months ago
0
Develop lee
#114
LeeBergstrand
closed
5 months ago
8
Refactor snakefile
#113
LeeBergstrand
closed
6 months ago
0
Refactor cli
#112
LeeBergstrand
closed
6 months ago
0
Move to Snakemake 8.0
#111
LeeBergstrand
opened
6 months ago
1
Refactor snakefile
#110
LeeBergstrand
closed
6 months ago
2
add Split snakefile
#109
LeeBergstrand
closed
6 months ago
0
update temp files with split snakemake files
#108
LeeBergstrand
closed
6 months ago
0
Update more_temp_files
#107
LeeBergstrand
closed
6 months ago
0
Hot-Fix Polca
#106
LeeBergstrand
closed
7 months ago
0
Hot-Fix Fix Polca
#105
LeeBergstrand
closed
7 months ago
0
split snakemake file into multiple.
#104
LeeBergstrand
closed
6 months ago
1
Add software demo to README
#103
jmtsuji
closed
7 months ago
0
Misc changes
#102
LeeBergstrand
closed
7 months ago
3
Should we consider adding a simple setting to completely skip short and/or long read QC?
#101
LeeBergstrand
opened
7 months ago
0
delete requirement to check for other polca files.
#100
LeeBergstrand
closed
7 months ago
4
Logo for rotary
#99
jmtsuji
closed
7 months ago
1
Bring the stitch_module branch up to date
#98
jmtsuji
closed
7 months ago
0
Parse medaka model from raw Nanopore reads
#97
jmtsuji
closed
3 months ago
6
Add basic PacBio support?
#96
jmtsuji
opened
7 months ago
0
Basic test suite for rotary
#95
jmtsuji
opened
7 months ago
2
Major rotary upgrades
#94
jmtsuji
closed
7 months ago
10
Check if decontamination genome references need to be in forward and reverse complement orientation
#93
jmtsuji
opened
7 months ago
0
Specify more temp files
#92
jmtsuji
closed
5 months ago
10
Report read QC stats
#91
jmtsuji
opened
7 months ago
12
Split rotary snakefile into multiple files
#90
jmtsuji
closed
5 months ago
3
Warn about multi-strain contamination based on CheckM2 stats
#89
jmtsuji
opened
7 months ago
0
Fix GTDB-Tk install error
#88
jmtsuji
closed
7 months ago
4
GTDB-Tk installation error
#87
jmtsuji
closed
7 months ago
2
README updates
#86
jmtsuji
closed
7 months ago
1
Detect if multiple genomes are present
#85
LeeBergstrand
closed
7 months ago
11
Nanopore Read Decontamination
#84
LeeBergstrand
opened
8 months ago
9
Add improvements to the readme.
#83
LeeBergstrand
closed
8 months ago
2
Short read improvements
#82
LeeBergstrand
closed
8 months ago
3
Add pigz flags to bbtools
#81
LeeBergstrand
closed
8 months ago
1
Tell users about config parameters available to bipass failed end repair.
#80
LeeBergstrand
closed
3 months ago
3
Validate config is up to date when running rotary run.
#79
LeeBergstrand
closed
3 months ago
4
Make a separate config file with database version information
#78
jmtsuji
opened
8 months ago
0
Add changes from develop to short read qc
#77
LeeBergstrand
closed
8 months ago
0
Add checkm
#76
LeeBergstrand
closed
8 months ago
1
Short read QC
#75
jmtsuji
closed
8 months ago
11
Make eggnog mapper use mmseqs2?
#74
LeeBergstrand
closed
8 months ago
3
Improve multi sample pathing
#73
LeeBergstrand
closed
8 months ago
4
Refactor aggregate_contigs function in rotary.smk for readability.
#72
LeeBergstrand
closed
3 months ago
3
Add multi sample capability.
#71
LeeBergstrand
closed
8 months ago
8
Refactor rotary cli
#70
LeeBergstrand
closed
8 months ago
2
Utilize sample tsv for single sample
#69
LeeBergstrand
closed
9 months ago
1
Improve logging of required coverage thresholds for contigs
#68
jmtsuji
opened
9 months ago
0
Refactor subcommand calls in rotary repair.py
#66
LeeBergstrand
closed
9 months ago
2
Bug fixes env pathing and file extentions
#65
LeeBergstrand
closed
9 months ago
0
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