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almlab
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SmileTrain
a 16s pipeline
MIT License
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Changed progressive_clustering to be compatible with new usearch8.0.1517
#79
spacocha
opened
9 years ago
1
refactor handling of pre-demultiplexed files. fix dry-run problems.
#78
elsherbini
closed
9 years ago
0
sort filenames so merging works correctly
#77
elsherbini
closed
9 years ago
0
add support for pre-demultiplexed files separated by sample
#76
elsherbini
closed
9 years ago
4
ref_gg uses wrong ID%
#75
swo
opened
9 years ago
0
seq table: small debugs
#74
swo
closed
9 years ago
0
seq table: improved format, now a class
#73
swo
closed
9 years ago
0
sequence barcode (aka "plate barcode") support
#72
swo
closed
9 years ago
5
Mapping file with a extra line on the end from excel
#71
spacocha
closed
9 years ago
1
Integrated JS and variable split ids for dbOTUs
#70
spacocha
closed
9 years ago
2
USEARCH chimera checking output seems wrong
#69
spacocha
opened
9 years ago
2
dbotus: progressive clustering, etc.
#68
swo
closed
9 years ago
2
config should not be a global variable
#67
swo
opened
9 years ago
0
Added Progressive clustering and splitting capabilities to complement db...
#66
spacocha
closed
9 years ago
1
more zcluster support
#65
andrew-enigma
closed
9 years ago
3
D different types of line breaks
#64
spacocha
closed
9 years ago
1
otu caller: small typo
#63
swo
closed
9 years ago
0
clean up otu_caller.py structure
#62
swo
opened
9 years ago
0
merging and redo
#61
swo
closed
9 years ago
0
Some way to store command-line flags as an analysis name to just do that analysis over and over
#60
spacocha
closed
9 years ago
1
Chimera-checking should have additional features
#59
spacocha
opened
9 years ago
0
refactored ssub
#58
swo
closed
9 years ago
0
ssub: more support for zcluster
#57
swo
closed
9 years ago
0
don't use popen in ssub
#56
swo
opened
9 years ago
0
otu caller: now recognizes user.cfg's cluster
#55
swo
closed
9 years ago
0
fixed tool scripts, submit options, etc.
#54
swo
closed
9 years ago
0
clean up command interfaces
#53
swo
opened
9 years ago
0
fixed coyote submission; added rev comp
#52
swo
closed
9 years ago
0
what are check_primers doing?
#51
swo
closed
9 years ago
1
convert fastq, read dist, zcluster
#50
swo
closed
9 years ago
0
argparse shows default values
#49
swo
closed
9 years ago
0
added some tools & default values to otu_caller help
#48
swo
closed
9 years ago
0
Add default values to the --help flag to know what's default without looking into the code
#47
spacocha
closed
9 years ago
2
ssub clusters should be separate modules
#46
swo
opened
9 years ago
0
check_fastq format has bad help message
#45
swo
closed
9 years ago
0
use subparsers
#44
swo
opened
9 years ago
0
n_cpus is a bad name
#43
swo
closed
9 years ago
1
otu caller: put intersect before merging
#42
swo
closed
9 years ago
0
dbotus breaks if you aren't in the same folder as the fastq file
#41
spacocha
opened
9 years ago
0
otu caller: changed mothur calls to strings
#40
swo
closed
9 years ago
0
--local and --dry_run should be mutually exclusive
#39
swo
closed
9 years ago
1
merge before removing primers?
#38
swo
closed
9 years ago
1
check intersect: counts line numbers first
#37
swo
closed
9 years ago
0
intersect re-added; other commands fixed
#36
swo
closed
9 years ago
0
shouldn't have to split if n_cpus == 1
#35
swo
closed
9 years ago
1
intersect should be integrated into primer removal?
#34
swo
closed
9 years ago
1
dbOTUs integrated
#33
swo
closed
9 years ago
0
unit tests for chimera removal
#32
swo
opened
10 years ago
0
chimera checking after otu calling
#31
swo
opened
10 years ago
0
Local running
#30
swo
closed
10 years ago
0
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