issues
search
abaizan
/
kodoja
Kodoja: identifying viruses from plant RNA sequencing data
MIT License
7
stars
6
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Kodoja failed unexpectedly
#44
sanchari24
opened
1 year ago
3
kodoja_build issue
#43
codespacebyaditya
opened
2 years ago
1
Retrieve Unclassified Sequences
#42
mariferrarini
closed
5 years ago
4
Kodoja_build.py to update genomes
#41
mariferrarini
closed
5 years ago
3
Ignore SSL certificate on TravisCI Python 2.7 tests
#40
peterjc
closed
5 years ago
0
Log exception when downloads fail
#39
peterjc
closed
5 years ago
0
Fix for Kaiju v1.7.0
#38
peterjc
closed
5 years ago
1
kaiju 1.7.0 renamed mkbwt to kaiju-mkbwt
#37
peterjc
closed
5 years ago
1
TravisCI: Python 2.7, NCBI download failing
#36
peterjc
closed
5 years ago
5
Species sequences and Genus sequences in virus_table.txt
#35
coralzhang
closed
5 years ago
5
virus_table.txt
#34
coralzhang
closed
5 years ago
1
How could I disable and skip the trimmomatic step?
#33
coralzhang
closed
5 years ago
2
v0.0.8 regression in kodoja_retrieve.py
#32
peterjc
closed
5 years ago
1
TaxID in combined_result column of kodoja_VRL.tsv as float
#31
peterjc
opened
6 years ago
1
v0.0.8 Output read ID not descr in kraken_VRL.txt
#30
peterjc
closed
6 years ago
3
Blank values (not zero) on older pandas
#29
peterjc
closed
6 years ago
3
Avoid pickle files for read number to name mapping
#28
peterjc
opened
6 years ago
4
only output FASTA/FASTQ from kodoja_retrieve.py
#27
peterjc
closed
6 years ago
1
Automated testing of kodoja_retrieve.py etc
#26
peterjc
closed
6 years ago
0
Record trimmomatic stdout in kodoja_search log file?
#25
peterjc
opened
6 years ago
0
Correct filtering of division.dmp etc
#24
peterjc
closed
6 years ago
0
Fix taxonomy filter script
#23
peterjc
closed
6 years ago
2
measure test coverage
#22
peterjc
opened
6 years ago
0
Small bug fixes for extra files in kodoja_build.py
#21
peterjc
closed
6 years ago
0
Use HTTPS over FTP; version bump
#20
peterjc
closed
6 years ago
0
Check kaiju_library.fmi in kodoja_build.py test
#19
peterjc
closed
6 years ago
1
Logging for retried downloads
#18
peterjc
closed
6 years ago
2
Increase retries, ramp up wait
#17
peterjc
closed
6 years ago
0
Check krakenDB_test/database.kdb in tests
#16
peterjc
closed
6 years ago
2
Retry downloads from NCBI FTP site.
#15
peterjc
closed
6 years ago
1
kodoja_build.py test changes
#14
peterjc
closed
6 years ago
4
Updating test taxonomy for kodoja_build.py
#13
peterjc
closed
6 years ago
1
Provide minimal NCBI taxonomy names.dmp and nodes.dmp
#12
peterjc
closed
6 years ago
1
Avoid calling shell commands for filesystem operations
#11
peterjc
closed
6 years ago
0
Column header naming
#10
peterjc
opened
6 years ago
2
Switch from /1 and /2 suffix to renaming reads by number only
#9
peterjc
closed
6 years ago
2
Include BioConda badge in README
#8
peterjc
closed
6 years ago
0
README bullet points and double-back-tick markdown
#7
peterjc
closed
6 years ago
0
Missing two empty columns of output (tab chars)
#6
peterjc
closed
6 years ago
2
Check / report Python dependencies in test script
#5
peterjc
closed
6 years ago
1
PE test fails, pandas ValueError: could not convert string to float: '100/1'
#4
peterjc
closed
6 years ago
4
Add TravisCI badge to README, and note in text
#3
peterjc
closed
6 years ago
0
Check dependencies in test script; Python 3 support
#2
peterjc
closed
6 years ago
0
Minor style changes and stricter flake8 settings
#1
peterjc
closed
6 years ago
1