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torognes
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swarm
A robust and fast clustering method for amplicon-based studies
GNU Affero General Public License v3.0
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Avoid producing microvariants if there is no amplicon of that length [dead end]
#83
frederic-mahe
closed
8 years ago
2
Change output sequences to upper case
#82
torognes
closed
7 years ago
3
Pacbio reads
#81
davidvilanova
closed
7 years ago
5
Residual variability in swarm clustering results
#80
frederic-mahe
closed
7 years ago
1
Segmentation fault on empty sequences
#79
frederic-mahe
closed
7 years ago
2
In rare cases Swarm does not terminate properly
#78
torognes
closed
7 years ago
2
Sanitize input options
#77
torognes
closed
7 years ago
3
Control the range of `d` values
#76
frederic-mahe
closed
7 years ago
2
Remove pairwise alignment settings from when using d =1
#75
frederic-mahe
closed
8 years ago
1
bug when using several threads
#74
frederic-mahe
closed
8 years ago
5
Return status should be 0 after -h and -v
#73
frederic-mahe
closed
8 years ago
1
Strip chr(13) from input fasta files
#72
ZeweiSong
closed
8 years ago
7
Make use of base quality score - Fastq support
#71
lerch-a
closed
8 years ago
7
;size=INT not being accepted
#70
jpearl01
closed
8 years ago
2
compiling swarm on osx 1.8.5
#69
colinbrislawn
closed
8 years ago
2
control number of generations, for the iterative growth process
#68
nikosdarzentas
closed
5 years ago
4
output of -w and -o are not consistent when run with -d 2
#67
nhoffman
closed
8 years ago
10
Amplicon length truncation
#66
vmikk
closed
8 years ago
7
Check that all input sequences are unique
#65
torognes
closed
7 years ago
2
digits transposed in file name of 2.1.5 binary
#64
nhoffman
closed
8 years ago
1
Potential problem reported by cppcheck
#63
frederic-mahe
closed
9 years ago
3
Compilation warning with gcc 4.9
#62
frederic-mahe
closed
9 years ago
1
dereplicating pooled specimens
#61
nhoffman
closed
9 years ago
9
Ability to process fastq files
#60
deprekate
closed
9 years ago
5
feature request: assume abundance = 1 when missing from sequence names
#59
nhoffman
closed
9 years ago
20
Allow ambiguous bases?
#58
psathyrella
closed
9 years ago
7
Sequence identifiers format, abundace annotation not found error
#57
jenspreem
closed
9 years ago
3
Clustering with d = 1 and replicates
#56
ghost
closed
8 years ago
6
Complete integration of the fastidious option?
#55
frederic-mahe
closed
7 years ago
7
IUPAC nucleotide ambiguity
#54
ThomasFort
closed
9 years ago
4
Minor inconsistencies with fastidious
#53
torognes
closed
9 years ago
4
Improve documentation of Fastidious option
#52
colinbrislawn
closed
9 years ago
4
Abundance annotation style should be maintained in the output fasta file
#51
frederic-mahe
closed
9 years ago
1
Galaxy wrapper for Swarm
#50
torognes
closed
8 years ago
2
Compilation issue with swarm 2.0.4
#49
frederic-mahe
closed
9 years ago
1
Use swarm for dereplication (-d 0)
#48
frederic-mahe
closed
9 years ago
2
Downstream analysis on otutable or biom file
#47
mdehollander
closed
6 years ago
9
Avoid SSE3 and SSSE3 dependency
#46
torognes
closed
9 years ago
3
Assigning taxonomy to swarm centroids
#45
colinbrislawn
closed
9 years ago
5
Rewrite search8.cc and search16.cc using intrinsics for portability
#44
torognes
closed
5 years ago
7
Chimera checking and swarm
#43
colinbrislawn
closed
9 years ago
22
Implement the new fastidious option
#42
torognes
closed
9 years ago
2
Add the OTU number to the output of the -b option
#41
frederic-mahe
closed
9 years ago
3
Integrate the swarm-breaker into the main swarm code
#40
torognes
closed
9 years ago
4
swarm_breaker.py sometimes hangs forever
#39
frederic-mahe
closed
9 years ago
2
swarm_breaker.py handles multi-line fasta files incorrectly
#38
torognes
closed
9 years ago
1
Sequence headers with multiple underscore characters cause problems
#37
torognes
closed
9 years ago
1
Read input from stdin if no filename is specified on the command line
#36
torognes
closed
9 years ago
1
Segmentation fault (or SIGABRT) with -a
#35
frederic-mahe
closed
9 years ago
3
Bug in the -b option output (critical)
#34
frederic-mahe
closed
9 years ago
2
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