issues
search
pirovc
/
genome_updater
Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy
MIT License
138
stars
14
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Unbound variable (line 253)
#96
iwilkie
opened
4 months ago
2
Empty *faa|missing files
#95
mwylerCH
opened
4 months ago
5
The number of GTDB complete genomes mismatched with that in official website due to some records are deleted in NCBI
#94
shenwei356
closed
1 month ago
5
Species representative selection criteria
#93
JensUweUlrich
closed
7 months ago
1
citation?
#92
rjsorr
closed
8 months ago
3
download issues
#91
rjsorr
closed
9 months ago
4
Download command not found in conda environment
#90
jpjarnoux
closed
9 months ago
6
Allow negation in taxonomy
#89
mbhall88
opened
1 year ago
1
faaling to download data from ncbi
#88
schlogl2017
closed
9 months ago
4
genome_updater version 0.6.3
#87
pirovc
closed
1 year ago
1
NCBI assembly summary now has 38 columns
#86
schorlton
closed
1 year ago
2
Bugfix/find type one letter
#85
pirovc
closed
1 year ago
0
Failed to download assembly_summary.txt
#84
schmittel
closed
1 year ago
7
v0.6.1 update GTDB release, using latest
#83
pirovc
closed
1 year ago
0
genome_updater version 0.6.0
#82
pirovc
closed
1 year ago
0
Feature/infra fixes
#81
pirovc
closed
1 year ago
0
Feature/folder structure ncbi
#80
pirovc
closed
1 year ago
0
questions on keep full taxonomy of downloaded genomes
#79
jianshu93
closed
1 year ago
1
genome_updater v0.5.2
#78
pirovc
closed
1 year ago
0
Failed to download gtdb taxonomy
#77
ohickl
closed
1 year ago
6
Parallel error
#76
drhoads
closed
1 year ago
23
Feature request: allow wildcard filtering based on assembly name
#75
jdwinkler-lanzatech
opened
2 years ago
4
Filter by Genbank features
#74
asumann
closed
2 years ago
1
Zero assemblies downloaded, with "awk: line 18: illegal reference to array filter"
#73
zreitz
closed
2 years ago
2
Script is not working on a 2022 MacBook Pro M1 Pro
#72
ltalignani
closed
2 years ago
3
add nr database as a -d option
#71
rjsorr
closed
2 years ago
1
/genome_updater.sh: illegal option -- P Invalid options
#70
rjsorr
closed
2 years ago
2
genome_updater v0.5.1
#69
pirovc
closed
2 years ago
1
Feature/write simplecov travis
#68
pirovc
closed
2 years ago
0
Bugfix/print header check as
#67
pirovc
closed
2 years ago
0
Feature/test top assemblies
#66
pirovc
closed
2 years ago
0
fix filter top assemblies
#65
shenwei356
closed
2 years ago
1
Top species assemblies do not contain that of subspecies
#64
shenwei356
closed
2 years ago
5
fix the regular expression to match the max assemblies number
#63
shenwei356
closed
2 years ago
2
genome_updater v0.5.0
#62
pirovc
closed
2 years ago
0
Feature/codecov
#61
pirovc
closed
2 years ago
1
Feature/reports
#60
pirovc
closed
2 years ago
0
Feature/better download tax
#59
pirovc
closed
2 years ago
0
Feature/general fixes
#58
pirovc
closed
2 years ago
0
Feature/check assembly summary
#57
pirovc
closed
2 years ago
1
Different number of entries in different query
#56
GreyGuoweiChen
closed
2 years ago
2
Feature/taxonomy options
#55
pirovc
closed
2 years ago
0
Feature/better gtdb integration
#54
pirovc
closed
2 years ago
0
Feature/general fixes impr
#53
pirovc
closed
2 years ago
0
Feature/update from history
#52
pirovc
closed
2 years ago
0
Feature/print better progress
#51
pirovc
closed
2 years ago
0
Parallel error when dowloading
#50
lshilab
closed
2 years ago
2
Filter issue in v0.4.1 while there's no problem in v0.2.5
#49
shenwei356
closed
2 years ago
2
v0.4.1
#48
pirovc
closed
2 years ago
0
Update static GTDB urls in script
#47
aistBMRG
closed
2 years ago
2
Next