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gbouras13
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pharokka
fast phage annotation program
MIT License
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Bioconda version is out of date
#310
marade
closed
9 months ago
2
database error
#309
mengyuan09876
closed
9 months ago
2
Pharokka fails on large dataset
#308
nelsonruth11
closed
8 months ago
4
phannote issues?
#307
raw937
closed
8 months ago
2
what gene should we use to put at +1 in a Stx-phage assembly
#306
splaisan
closed
10 months ago
4
FR: add a pharokka_plotter.py argument to select the contig to be plotted in case more than one contig in the assembly
#305
splaisan
closed
10 months ago
2
Cannot get pharokka databases installed
#304
Jlee795
closed
8 months ago
8
PHAROKKA introducing dataframe and its dtype into NCBI Feature Table (.tbl) in each Loop.
#303
deinotoxazumab
closed
8 months ago
5
add plotting labels clarification
#302
gbouras13
closed
11 months ago
0
Pharokka fails when contig input file ends in .fa, runs when file ends in .fasta
#301
nelsonruth11
closed
11 months ago
1
pharokka protein crashed after completing mmseqs searches
#300
luisalbertoc95
opened
11 months ago
9
External tools Fine parameter tuning
#299
iferres
closed
8 months ago
4
v 1.5.1
#298
gbouras13
closed
11 months ago
0
AttributeError: module 'pyrodigal' has no attribute 'OrfFinder'
#297
gbouras13
closed
11 months ago
2
pharokka proteins mash skip check
#296
gbouras13
closed
1 year ago
0
spell Larralde correctly
#295
gbouras13
closed
1 year ago
0
Version v1.5.0. Fixes #290. Fixes #293
#294
gbouras13
closed
1 year ago
0
Expanding initial checks for user friendliness
#293
thauptfeld
closed
1 year ago
0
Use a multithreaded pool to run Pyrodigal in parallel
#292
althonos
closed
1 year ago
2
VFDB databases are missing
#291
sallybyers
closed
1 year ago
6
Error calling tRNAscan-SE
#290
asierFernandezP
closed
1 year ago
19
update release [skip ci]
#289
gbouras13
closed
1 year ago
0
Update HISTORY.md
#288
gbouras13
closed
1 year ago
0
Patch fixes #286
#287
gbouras13
closed
1 year ago
0
Pharokka doesn't look for the good file in meta mode
#286
rdenise
closed
1 year ago
3
Quick question
#285
r4carson
closed
1 year ago
2
minor readme changes [skip ci]
#284
gbouras13
closed
1 year ago
0
Deve
#283
gbouras13
closed
1 year ago
0
fix docs [skip ci]
#282
gbouras13
closed
1 year ago
0
fix contig fast bug from vfdb/card counts
#281
gbouras13
closed
1 year ago
0
card and vfdb functions count streamline and fix 0s
#280
gbouras13
closed
1 year ago
0
Proteins tmp outdir removal
#279
gbouras13
closed
1 year ago
0
add tests updating for genbank
#278
gbouras13
closed
1 year ago
0
more history changes [skip ci]
#277
gbouras13
closed
1 year ago
0
Fixes to `--genbank` to handle custom CDS calls
#276
gbouras13
closed
1 year ago
0
Deve v1.4.0 Fixes #249 #263 #267 #270 #271 and adds many other features
#275
gbouras13
closed
1 year ago
0
install_databases.py downloads unneeded hidden files
#274
jowodo
closed
1 year ago
2
Test data
#273
gbouras13
closed
1 year ago
0
make dependabot happy
#272
gbouras13
closed
1 year ago
0
Add validation if out directory exists
#271
gbouras13
closed
1 year ago
1
Plotter inclusive of AMR genes and VFs?
#270
mhmism
closed
1 year ago
3
Allow for non standard translation table
#269
alegione
closed
1 year ago
1
Fixed GBK translation when non-11 coding tables used
#268
alegione
closed
1 year ago
3
Sequences (contigs) ids should be equal in gff's table and fasta section
#267
iferres
closed
1 year ago
2
MMSeqs2 error on PHROG database
#266
tenguzame
closed
1 year ago
1
galaxy2
#265
gbouras13
closed
1 year ago
0
galaxy
#264
gbouras13
closed
1 year ago
0
--label_hypotheticals
#263
hmdaahmd
closed
1 year ago
3
fixes #261 adds bioconda badge
#262
gbouras13
closed
1 year ago
0
specify in documentation that --terminase_start requires strand-specific coordinate
#261
acvill
closed
1 year ago
1
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