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apcamargo
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genomad
geNomad: Identification of mobile genetic elements
https://portal.nersc.gov/genomad/
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Marker classfication and other stuff
#57
AhmedElsherbini
closed
6 months ago
6
KeyError: 'ATAACA' happened in Executing genomad marker-classification.
#56
YANG-Jiwei
closed
7 months ago
9
[Question] Taxonomy on a viral bin with multiple contigs
#55
jolespin
closed
7 months ago
1
cudnn error in nn-classification
#54
pck00
closed
7 months ago
3
error with end-to-end
#53
abdo3a
opened
7 months ago
5
Does geNomad currently support training new models?
#52
a-piece-of-teemo
closed
7 months ago
10
Unable to run
#51
WenluYIN
opened
7 months ago
4
Error running Genomad 1.7.1
#50
mhmism
opened
8 months ago
2
Take circularity into account when applying post-classification filters
#49
apcamargo
opened
8 months ago
0
Support for GFF and GBK outputs
#48
apcamargo
opened
8 months ago
0
Finding chimeric sequences
#47
bhimbbiswa
closed
8 months ago
4
Step skipping doesn't work properly in the classification modules when the output of `annotate` changes
#46
apcamargo
opened
8 months ago
0
Interpretation of Results
#45
owbarber
closed
8 months ago
3
Fasta contains multiple entries with the same identifier
#44
jsming1996
closed
8 months ago
1
Issues running genomad
#43
david1ibarra
opened
8 months ago
1
Assistance Needed: Unexpected Error and Output Truncation During geNomad Tool Execution
#42
david1ibarra
opened
8 months ago
4
Error: prokka: Failed to download resource "aragorn"
#41
AnnaaaaaaaaV
closed
8 months ago
7
Understanding Inputs and Outputs
#40
sophiaaredas
closed
8 months ago
2
Possibility to include NAs in taxonomy csv format for easier parsing?
#39
LanderDC
closed
2 months ago
10
enable-score-calibration option
#38
elozanoe
closed
3 months ago
7
Input file does not exist error
#37
Elle-ctricity
closed
9 months ago
4
aragorn package does not exist
#36
sophiaaredas
closed
9 months ago
5
question about nn-classification
#35
lilinzhou
opened
9 months ago
3
mmseqs prefilter error: database has wrong type
#34
ShailNair
closed
9 months ago
2
Taxonomy changed when input contigs are different
#33
xwu35
closed
9 months ago
10
FileNotFoundError
#32
chengzhongyi8
closed
10 months ago
5
Provirus detection changes when more input is given
#31
nikolasbasler
closed
10 months ago
3
Is it safe to run genomad directly on nanopore R10.4.1 long reads?
#30
xinehc
opened
10 months ago
1
Would there be a smaller database available to use for testing?
#29
AnnaSyme
closed
10 months ago
6
Is there a way to get the annotate outputs in a genbank format file?
#28
liliancaesarbio
opened
11 months ago
9
nn-classification module uses all available CPUs instead of the limit set by --threads
#27
jamesck2
closed
11 months ago
9
Is it better to run geNomad on single genome assemblies?
#26
joelwwh
closed
11 months ago
1
mmseqs2 prefilter failed: No k-mer could be extracted for the database genomad_db/genomad_db
#25
haleyhallowell
closed
12 months ago
4
Does prediction with no coordinates indicate the whole sequences is a viral sequence?
#24
shenwei356
closed
1 year ago
2
How to organize the file structure of geNomad database
#23
shenwei356
closed
1 year ago
1
Can genomad be applied to the metagenome bin?
#22
qkqk-hub
closed
1 year ago
2
mmseqs2 prefilter requires too much memory
#21
Bgi-zsy
closed
1 year ago
3
Long fasta headers with white spaces may interfere with downstream processing
#20
Werner0
closed
1 year ago
4
Difference between "Unclassified" and "Viruses" taxonomy?
#19
ecampbell50
closed
1 year ago
7
decrease in the number of hits with the new version
#18
kayanac
closed
1 year ago
20
Too many threads used in numpy and tensorflow
#17
tsp-kucbd
closed
1 year ago
2
Tenserflow error for nn-classification
#16
michoug
closed
1 year ago
4
UnicodeEncodeError
#15
cody-mar10
closed
1 year ago
3
Processing many genomes
#14
franciscozorrilla
closed
1 year ago
1
provirus info appears in find_proviruses/provirus.tsv but lost in summary/summary.tsv
#13
yumenghao2021
closed
1 year ago
4
AttributeError
#12
deminatanja
closed
1 year ago
6
mmseqs2: returned non-zero exit status 1.
#11
MonicaSteffi
closed
1 year ago
19
`OSError: Could not find/load shared object file: libllvmlite.so` from broken conda-forge package. Found fix with using numba channel.
#10
jolespin
closed
1 year ago
2
Non-detailed taxonomy classification. Possibility of IMG/VR database integration
#9
poursalavati
closed
1 year ago
10
KeyError: 'provirus_names' when running genomad score_calibration
#8
rdenise
closed
1 year ago
3
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