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nlapier2
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Metalign
Metalign: efficient alignment-based metagenomic profiling via containment min hash
MIT License
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Discrepancy in Abundances in Sensitive Mode
#45
echolley31
opened
5 months ago
0
Missing Files?
#44
echolley31
opened
7 months ago
2
After conda installation, metalign command does not work
#43
mahmudhera
closed
1 year ago
2
Add threads argument to the call of StreamingQueryDNADatabase.py.
#42
SamGallop-NBI
opened
1 year ago
0
How are interleaved paired reads treated in Metalign?
#41
aminards
opened
2 years ago
0
Metalign run error
#40
premkrishnan
opened
3 years ago
5
Build a customized database?
#39
chunyuma
opened
3 years ago
11
setup_libraries.sh file missing
#38
arvidgollwitzer
closed
4 years ago
2
Handling long reads
#37
nlapier2
opened
4 years ago
1
Minimizer pre-computing
#36
nlapier2
opened
4 years ago
0
setup_data.sh not in bioconda release
#35
dkoslicki
opened
4 years ago
1
Update Wiki and readmes
#34
dkoslicki
opened
4 years ago
1
Possible missing genomes?
#33
vrou1995
opened
4 years ago
2
Large Repo Size
#32
nlapier2
opened
4 years ago
0
Using paired read files as input
#31
vrou1995
closed
4 years ago
1
Non-microbial organisms in training database
#30
dkoslicki
opened
4 years ago
1
Training file names contain “.gz.gz”
#29
dkoslicki
closed
4 years ago
3
Add option to save the minimap2 output to file (instead of just streaming it through)
#28
dkoslicki
opened
4 years ago
0
Refactor how CMash is called
#27
dkoslicki
closed
4 years ago
1
Conda installation version?
#26
Anto007
closed
4 years ago
1
Will need to re-train the default database
#25
dkoslicki
opened
4 years ago
4
KMC fasta vs multi-fasta error
#24
dkoslicki
opened
4 years ago
1
WIP: Fix #16 allow KMC and Minimap2 binaries on user path
#23
peterk87
closed
4 years ago
3
Building the Metalign database from different sources
#22
nlapier2
opened
4 years ago
4
db_info.txt read multiple times during normal run of Metalign
#21
peterk87
opened
4 years ago
2
Version number, setup.py, github, PyPI, Conda releases
#20
peterk87
closed
4 years ago
7
setup.py and PyPI, Bioconda deployment?
#19
peterk87
closed
4 years ago
1
ZeroDivisionError: float division by zero
#18
luhugerth
opened
4 years ago
4
Use Python logging module?
#17
peterk87
opened
4 years ago
1
Allow use of system/user installed Minimap2/KMC/etc
#16
peterk87
closed
4 years ago
5
Zenodo for large data archive?
#15
peterk87
closed
4 years ago
8
Permission denied for docker pull
#14
Anto007
opened
4 years ago
6
Can metalign be used for profiling (micro)eukaryotes?
#13
Anto007
closed
4 years ago
3
Create tutorial scripts that show common use cases
#12
dkoslicki
opened
4 years ago
2
Script hanging problem (and proposed solution)
#11
dkoslicki
closed
4 years ago
8
File placements not consistent
#10
dkoslicki
closed
4 years ago
1
Threads option isn't inherited by KMC
#9
dkoslicki
closed
5 years ago
1
Indicate to user where the subset database exists
#8
dkoslicki
closed
4 years ago
2
Don't make metalign.py executable
#7
dkoslicki
closed
5 years ago
1
Add command line argument descriptions
#6
dkoslicki
closed
5 years ago
2
Add capability to operate on compressed reads
#5
dkoslicki
closed
5 years ago
1
CMash need not be run with kmer sizes down to 30
#4
dkoslicki
closed
4 years ago
5
FASTA and FASTQ support
#3
dkoslicki
closed
5 years ago
1
KMC bad_alloc error
#2
dkoslicki
closed
5 years ago
1
Missing setup.sh
#1
dkoslicki
closed
5 years ago
1