khyox/recentrifuge
Recentrifuge: robust comparative analysis and contamination removal for metagenomics
PythonNOASSERTION
Issues
- 2
Add threads options, why and how
#54 opened by jfouret - 5
- 0
taxonomy files for common 16S datasets?
#52 opened by faylward - 1
Error code 13?
#53 opened by BZed81 - 3
- 9
ImportError: cannot import name 'SequentialSequenceWriter' from 'Bio.SeqIO.Interfaces'
#49 opened by pimarin - 1
Rextract from Kraken2 output
#46 opened by buiguesj - 1
Score understanding
#44 opened by lvelosuarez - 1
(question) produced output
#43 opened by arz19893 - 1
abundance table as output
#41 opened by rjsorr - 11
- 1
- 1
float deprecated in numpy 1.24
#47 opened by Electrocyte - 0
refasplit output files with non-padded zeros
#45 opened by khyox - 3
interpreting log file for contamination removal
#40 opened by rjsorr - 3
-k for multiple directories of .krk files?
#37 opened by rjsorr - 0
- 1
definition of contaminat level for removal?
#39 opened by rjsorr - 0
rextract: add option to get the unclassified reads
#28 opened by khyox - 3
rextract: ZeroDivisionError
#36 opened by shrivastavabhishek - 5
Compatibility with Ganon?
#35 opened by rjsorr - 2
ZeroDivisionError
#34 opened by jagos01 - 2
Data from article "Recentrifuge: Robust comparative analysis and contamination removal for metagenomics"
#33 opened by kla44 - 1
unclassified reads in rextract
#32 opened by comixwang - 10
parameter -y/--minscore in rextract
#31 opened by fancyge - 7
rextract: zipped fastq files
#30 opened by fancyge - 4
min() arg is an empty sequence [error]
#29 opened by JChristopherEllis - 8
rextract: read retrieval failed
#27 opened by webbchen - 6
No sequence passed the filter error
#13 opened by mhyleung - 1
- 1
- 5
KeyError: 'STRAIN'
#23 opened by abomba - 3
- 3
ZeroDivisionError/Centrifuge
#22 opened by ganiatgithub - 3
divided by zero error - fault by using krakenuniq?
#18 opened by BioNij - 3
- 0
- 2
- 3
- 6
- 2
export PDF from recentrifuge results?
#6 opened by HanZhenZ - 5
Using centrifuge premade (.cf) database
#12 opened by benkraj - 5
retest fails on MacOS
#11 opened by BenKaehler - 1
- 3
CSV output
#9 opened by my-serendipity - 6
Excel output with empty columns
#8 opened by blwe - 2
Test files?
#7 opened by sminot - 5
export .png?
#3 opened by devonorourke - 2
what the unassgined means?
#5 opened by yeli7068 - 4
centrifuge db
#4 opened by shlomobl