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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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Using SWARM on zOTUs instead of dereplicated sequences?
#183
nick-dil
closed
22 hours ago
2
Refactor Bloom filter code
#182
torognes
opened
5 months ago
0
correct example in the man
#181
vmikk
closed
7 months ago
2
swarm terminates if any sequence in the input fasta file has an N
#180
killidude
closed
8 months ago
2
Option to output cluster member ids/sequence id?
#179
koh-joshua
closed
9 months ago
3
fastidious boundary applies to the consolidated cluster mass?
#178
frederic-mahe
closed
11 months ago
1
risk of silent 8-bit unsigned integer overflow in score matrix
#177
frederic-mahe
closed
11 months ago
5
Option to exclude seeds or clusters with low abundance
#176
torognes
opened
1 year ago
1
Seeds not in same order as clusters in output files
#175
andnischneider
closed
1 year ago
2
integer division might be one byte too small in some cases
#174
frederic-mahe
closed
1 year ago
14
Invalid numeric argument for option -t or --threads
#173
Gian77
closed
1 year ago
8
uc file question
#172
dougwyu
closed
2 years ago
7
maximal header length
#171
frederic-mahe
closed
1 year ago
1
Refine readme citations
#170
lczech
closed
2 years ago
3
Compiling fails on Windows
#169
torognes
closed
2 years ago
3
OTU table without abundance values
#168
AshleyZhao20
closed
2 years ago
6
Issues with plotting: OTU not found
#167
naurasd
closed
2 years ago
3
way too many clusters?
#166
Gian77
closed
2 years ago
7
Add swarm3 citation
#165
lczech
closed
3 years ago
3
Link to new swarm 3 paper
#164
lczech
closed
3 years ago
3
documentation: maximal input sequence length
#163
frederic-mahe
closed
2 years ago
9
table formats for making OTU table from swarm results
#162
SanniH
closed
3 years ago
2
Roadmap
#161
frederic-mahe
closed
1 year ago
9
Incorrect results with long sequences, very high gap penalties, and d>1
#160
torognes
closed
3 years ago
9
Installation issues
#159
naurasd
closed
3 years ago
8
continuous integration service
#158
frederic-mahe
closed
2 years ago
2
swarm 3.0 on conda
#157
Gian77
closed
3 years ago
3
clustering of huge amount of reads
#156
mariabernard
closed
3 years ago
1
macros for min() and max()?
#155
frederic-mahe
closed
3 years ago
3
magic value?
#154
frederic-mahe
closed
3 years ago
2
restrict -x usage to d > 1
#153
frederic-mahe
closed
4 years ago
2
Get rid of CityHash?
#152
torognes
closed
4 years ago
3
Some helgrind tests fail when swarm is compiled for coverage testing
#151
torognes
closed
4 years ago
6
more amplicons with -d 2 than -d 1?
#150
KabitaBaral1
closed
4 years ago
2
swarm 3.0: cppcheck report (low priority)
#149
frederic-mahe
closed
4 years ago
2
Empty internal files after running swarm with -d 0
#148
dcm9123
closed
4 years ago
5
amplicon sequence reconstruction with swarm?
#147
KabitaBaral1
closed
4 years ago
4
code coverage 2: the gnarly cases
#146
frederic-mahe
closed
4 years ago
32
Does swarm work with nanopore short amplicons?
#145
dcm9123
closed
4 years ago
3
code modernization (long-term task, very low priority)
#144
frederic-mahe
closed
4 years ago
1
code coverage for algod1.cc
#143
frederic-mahe
closed
4 years ago
3
nw.cc: last lines not triggered by a test
#142
frederic-mahe
closed
4 years ago
4
db.cc: condition is always true
#141
frederic-mahe
closed
4 years ago
7
code coverage for db.cc
#140
frederic-mahe
closed
4 years ago
2
code coverage for derep.cc
#139
frederic-mahe
closed
4 years ago
4
support ambigous nucleotides N
#138
sfehrmann
closed
4 years ago
2
swarm 3.0 Floating point exception for bloom-bits values 2, 3 and 4
#137
frederic-mahe
closed
4 years ago
3
avoid variable shadowing, same naming scheme as other local variables
#136
frederic-mahe
closed
4 years ago
1
Code Quality Benchmark (softwipe)
#135
frederic-mahe
closed
4 years ago
25
DNA base characters other than ACGT
#134
kemin711
closed
5 years ago
1
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