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bonsai-team
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matam
Mapping-Assisted Targeted-Assembly for Metagenomics
GNU Affero General Public License v3.0
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Problem when trying to use RDP and UNITE DB as reference
#68
quetjaune
closed
5 years ago
2
Be less stringent when filtering RDP results
#67
loic-couderc
closed
5 years ago
3
The 16 bacterial species simulated dataset is missing from the conda package
#66
loic-couderc
closed
5 years ago
0
Failed ton install Matam from Conda package
#65
pgdurand
closed
5 years ago
6
install matam on HPC without sudo permissions
#64
quetjaune
closed
5 years ago
2
Error in matam_assembly on Docker when running example file
#63
rachelleLim
opened
6 years ago
5
MATAM aborting with non-zero return code: -8
#62
rotoscan
closed
6 years ago
3
Error in taxonomic assignment
#61
jmtsuji
closed
5 years ago
5
anaconda salford_systems channel does not exist anymore
#60
loic-couderc
closed
6 years ago
3
Expose the RDP cutoff as a matam_assembly parameter
#59
loic-couderc
closed
5 years ago
0
RDP nodes under a confidence threshold have to be tag "unclassified"
#58
loic-couderc
closed
6 years ago
0
Integrate Travis CI
#57
loic-couderc
closed
6 years ago
0
sort: unrecognized option '--parallel'
#56
zhssakura
closed
6 years ago
11
Be more explicit when a command using runner module failed
#55
loic-couderc
closed
4 years ago
0
Update krona visualization to take into account RDP confidence scores
#54
loic-couderc
opened
6 years ago
1
Add some descriptive statistics to matam logs
#53
loic-couderc
opened
6 years ago
0
Give the choice of the clustering tool used to prepare the database between vsearch and sumaclust
#52
loic-couderc
opened
6 years ago
0
Symlink for final fasta file is not done when --perform taxonomic_assignment is ommitted
#51
loic-couderc
closed
6 years ago
0
Allow to resume from taxonomic_assignment step
#50
loic-couderc
closed
6 years ago
0
LCA labelling error with custom database
#49
loic-couderc
opened
6 years ago
0
Do no limit the debian version for docker image
#48
loic-couderc
closed
6 years ago
0
Do no fix the debian version used by docker
#47
loic-couderc
closed
6 years ago
0
Ovgraphbuild compilation issue with gcc-6
#46
loic-couderc
closed
6 years ago
0
SGA logging
#45
loic-couderc
opened
6 years ago
0
Docker is not building anymore
#44
loic-couderc
closed
6 years ago
1
Check dependencies before going any further
#43
loic-couderc
closed
4 years ago
1
Use GitLab as our main repository manager ?
#42
ppericard
opened
6 years ago
1
Add a step to compare taxonomic assignments from multiple datasets
#41
ppericard
closed
6 years ago
0
BIOM format
#40
ycl6
opened
6 years ago
3
Standardize RDP taxa
#39
ppericard
closed
6 years ago
1
No valid binary found for sga
#38
ycl6
closed
6 years ago
6
Add support for gzipped read files
#37
ppericard
opened
6 years ago
0
Problem completing installation (download-traindata)
#36
ycl6
closed
6 years ago
4
Expose the min scaffold length as a parameter
#35
ppericard
closed
6 years ago
0
Allow dynamic reduction of the coverage for highly covered references
#34
loic-couderc
closed
6 years ago
3
Improve scaffolding by using paired-end reads
#33
ppericard
opened
6 years ago
0
Look into SGA scaffolding step if paired-end reads are used
#32
ppericard
opened
6 years ago
1
Better handling paired-end reads
#31
ppericard
opened
6 years ago
0
Make the krona tabulated file an output file
#30
ppericard
closed
6 years ago
0
Abundance computing: Add warning for scaffolds with abundance=0
#29
ppericard
opened
6 years ago
3
Rethink the README
#28
loic-couderc
closed
5 years ago
2
preferred installation method
#27
rchikhi
closed
5 years ago
3
Duplicate the STDOUT and STDERR outputs in a log file
#26
ppericard
closed
6 years ago
2
Code deduplication
#25
loic-couderc
opened
7 years ago
0
The components assembly module has to be "assembler agnostic"
#24
loic-couderc
closed
7 years ago
4
Bug in RDP parsing leads to false taxa in Krona
#23
ppericard
closed
7 years ago
0
Improve output files visibility
#22
ppericard
closed
6 years ago
0
Improve files naming
#21
ppericard
closed
7 years ago
2
Docker classification issue:
#20
EisenRa
closed
7 years ago
4
Getting no scaffold > 500bp should raise an error and exit
#19
ppericard
closed
7 years ago
0
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