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ncbi
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vadr
Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation
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bug: vadr annotation erroneous coordinates/matchs for avian coronavirus
#89
FTouzain
opened
2 days ago
5
Model info file: alternative_ftr_set_subn values don't work properly if they contain whitespace
#88
nawrockie
opened
1 month ago
0
v-annotate.pl cannot be run with apptainer exec using the VADR Biocontainers Apptainer/Singularity image
#87
peterk87
opened
2 months ago
0
Adds annotate-tbl2gff.pl miniscript
#86
nawrockie
closed
3 months ago
0
Adds annotate-tbl2gff.pl script
#85
nawrockie
closed
3 months ago
1
v-annotate.pl bug: cdsstopp alert causes script to fail if early stop position exceeds CDS model length
#84
nawrockie
closed
3 months ago
2
Frameshifts for 5' truncated alignments beginning with an insert are mishandled
#83
nawrockie
closed
4 months ago
1
Outdated MODEL-VERSIONS.txt previnting automated model download
#82
Codes1985
closed
4 months ago
2
Extra header lines in .vadr.sqa
#81
garfinjm
closed
4 months ago
2
v-build.pl 1.6.3 fails on mac os/x
#80
nawrockie
closed
4 months ago
1
compatibility with `-` and `.` in input assemblies
#79
kapsakcj
closed
4 months ago
2
Bioconda - 1.6.3 broken symlink
#78
nawrockie
closed
4 months ago
3
Unable to build a model(NC_006273)
#77
voidbag
closed
4 months ago
1
Installation Issue 1.5.1
#76
jowodo
closed
4 months ago
8
Installation Documentation: vadr-install.sh download link
#75
jowodo
closed
1 year ago
1
Problem with building a model library
#74
Reshetnikoff
closed
1 year ago
4
v-annotate.pl fails with 'unable to open file' error on mac os/x
#73
nawrockie
closed
1 year ago
1
Bug: codon_start and truncation flag (<) missing in .tbl for multi-segment CDS if sequence begins after end of segment 1
#72
nawrockie
closed
1 year ago
1
Bug: early stops misreported for multi-segment CDS
#71
nawrockie
closed
1 year ago
1
Bug: v-annotate.pl does not report cdsstopn for early in-frame stop codons in 3' truncated CDS if they are the final 3 nt of the input sequence
#70
nawrockie
closed
1 year ago
3
Incorrect reporting of short frameshifts in 5' truncated CDS in rare cases
#69
nawrockie
closed
1 year ago
1
Bug in parse_blast.pl script causes max length deletion to be incorrectly reported in rare cases
#68
nawrockie
closed
1 year ago
1
Is there a database built for most viruses?
#67
NailouZhang
closed
1 year ago
2
ERROR in sqf_EslTranslateCdsToFastaFile, problem translating CDS feature, unable to find expected translated sequence in EU156171/EU156171.vadr.cds.esl-translate.2.fa:
#66
NailouZhang
closed
2 years ago
3
ERROR in vdr_EutilsFetchToFile, problem fetching NC_063383.1 (undefined)
#65
NailouZhang
closed
2 years ago
0
Unable to build a model
#64
anilsurathu
closed
2 years ago
2
ERROR in utl_RunCommand() in vadr 1.5 installed via conda
#63
inspirewind
closed
1 year ago
18
Problem about fetching and parsing protein feature table file(s)
#62
hgwu80
closed
1 year ago
9
Bug: parse_blast.pl incorrectly detects strand if alignment line length is 1
#61
nawrockie
closed
2 years ago
1
problem with git clone corona on bitbucket
#60
FTouzain
closed
2 years ago
2
conda/mamba installation improvement
#59
FTouzain
closed
7 months ago
5
cdsstopp can be reported for stop codon that overlaps with replaced region (due to -r)
#58
nawrockie
closed
2 years ago
1
Error: summed psi of split states in node 32146 not 1.0 but : 1.001000
#57
Zjianglin
closed
1 year ago
8
VADR doesn't detect annotated segments
#56
halabikeren
closed
2 years ago
4
Error in v-build.pl on example command
#55
halabikeren
closed
2 years ago
2
VADR predicted nested genes, prevents submission to ENA
#54
taltman
opened
2 years ago
4
VADR produces qualifier with invalid value
#53
taltman
opened
2 years ago
4
VADR doesn't annotate second segment of segmented CoV genome
#52
taltman
opened
2 years ago
6
Understanding `misc_feature` with no qualifiers
#51
taltman
closed
2 years ago
4
Double-entries in `.tbl` file
#50
taltman
closed
2 years ago
2
Updates expected files for fixes to length string in FS error messages
#49
nawrockie
closed
2 years ago
0
VADR exits due to limited memory, but doesn't report this to the user
#48
taltman
closed
2 years ago
5
`ERROR in output_feature_table`
#47
taltman
closed
2 years ago
3
Ambigs not ns
#46
nawrockie
closed
2 years ago
1
Ambigs not ns
#45
nawrockie
closed
2 years ago
0
Test failed when running `do-all-tests.sh` with VADR 1.3
#44
taltman
closed
2 years ago
3
Error in install from Inline module
#43
minhtrung1997
closed
4 months ago
10
To generate GenBank format of a complete genome of SARS-CoV2 variants
#42
shakti83kumar
closed
2 years ago
2
Documentation: vadr-map-model-coords.pl command in wiki
#41
garfinjm
closed
3 years ago
1
Consider adding a script to download models
#40
rpetit3
closed
3 years ago
2
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