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althonos
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pyrodigal
Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!
https://pyrodigal.readthedocs.org
GNU General Public License v3.0
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command line replacement for prodigal
#56
alexcritschristoph
closed
1 week ago
2
Mask sequences with trailing `N`
#55
ohickl
closed
1 month ago
3
Feature request: Make assumptions from ambiguous bases in translation
#54
schorlton-bugseq
closed
1 month ago
9
`sequence_id` used differently in translation and GFF outputs?
#53
schorlton-bugseq
closed
1 month ago
3
module 'pyrodigal' has no attribute 'OrfFinder'
#52
EmiCA22
closed
4 months ago
1
Add CLI option to disable translation of stop codons
#51
zclaas
closed
5 months ago
0
CLI option to write amino acids without stop codon
#50
zclaas
closed
5 months ago
1
Some tests are skipped 'requires machine with SSE2 support' on the system which does have SSE2
#49
yurivict
closed
5 months ago
2
example for gene annotation on a MAG
#48
Hocnonsense
closed
7 months ago
2
gzip support
#47
jianshu93
closed
7 months ago
1
BrokenProcessPool
#46
oschwengers
closed
8 months ago
6
add ORGANISM label to GBK output
#45
GeoMicroSoares
opened
9 months ago
1
Error for contigs that do not contain coding regions using -p meta
#44
geronimp
closed
9 months ago
2
selenoproteins?
#43
mallen6
opened
9 months ago
2
different result comparing to prodigal
#42
zzsunday
opened
10 months ago
3
Conda availability of 2.2.0 and 2.3.0 restricted to Python 3.11
#41
oschwengers
closed
10 months ago
6
[2.3.0] Build fails: 'cpython/unicode/PyUnicode_New.pxd' not found, etc
#40
yurivict
closed
8 months ago
2
prodigal strange XXXX output
#39
jianshu93
closed
1 year ago
3
Tests failing in version 2.2.0 under Archlinux
#38
kbipinkumar
closed
1 year ago
5
Bioconda build on OSx after recent changes
#37
raufs
closed
1 year ago
7
[Feature request] Add support for --jobs in CLI
#36
jolespin
closed
1 year ago
1
[Feature request] Support for stdin
#35
jolespin
opened
1 year ago
5
Alternative translation tables
#34
Matt-Schmitz
closed
1 year ago
5
tests failing in archlinux
#33
kbipinkumar
closed
1 year ago
1
add gene size parameters to CLI
#32
cjprybol
closed
1 year ago
2
min_gene option in CLI
#31
cjprybol
closed
1 year ago
3
Pyrodigal in parallel
#30
rhysnewell
closed
1 year ago
4
Non-deterministic behaviour
#29
aaronmussig
opened
1 year ago
1
Difference between Pyrodigal 2.0.4 and Prodigal 2.6.3
#28
pchaumeil
closed
11 months ago
4
Difference between Pyrodigal 2.0.3 and Pyrodigal 2.6.3
#27
pchaumeil
closed
1 year ago
4
Inconsistent gene calls between Pyrodigal-2.0.2 and Prodigal-2.6.3+31b300a
#26
aaronmussig
closed
1 year ago
6
Docs don't explain how to run tests
#25
yurivict
closed
1 year ago
4
Add additional gene models to the metagenome mode
#24
apcamargo
closed
10 months ago
11
Bioconda OSX builds
#23
oschwengers
closed
1 year ago
4
Duplicate extraction of edge nodes on genomes with a start codon on edge
#22
althonos
closed
1 year ago
1
Inconsistent gene predictions for Pyrodigal and *fixed* Prodigal
#21
oschwengers
closed
1 year ago
18
Sequence index is not preserved in multithread mode
#20
zdk123
closed
1 year ago
2
Inconsistent start score computed for some genes
#19
althonos
opened
1 year ago
1
GFF seqid may violate gff3 spec
#18
zdk123
closed
1 year ago
4
Bioconda update to v1.1.0 is blocked
#17
jhahnfeld
closed
2 years ago
2
install on arm failure
#16
jianshu93
closed
2 years ago
3
[ImgBot] Optimize images
#15
imgbot[bot]
closed
2 years ago
0
Imperfect Replication of Prodigal
#14
KGerhardt
closed
2 years ago
4
Different versions yield different ORFs
#13
celiosantosjr
closed
2 years ago
7
Excessive memory use
#12
KGerhardt
closed
2 years ago
5
Implement customization of the minimum gene size
#11
althonos
closed
2 years ago
1
Is it possible to exclude amino acids predicted as unknown - 'X'
#10
linda5mith
closed
2 years ago
4
Fixing paper metadata
#9
arfon
closed
2 years ago
1
rust prodigal
#8
jianshu93
closed
2 years ago
2
[ImgBot] Optimize images
#7
imgbot[bot]
closed
2 years ago
1
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