jenniferlu717 KrakenTools issues

jenniferlu717 / KrakenTools

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

GNU General Public License v3.0

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issues

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extract_kraken_reads.py ValueError: invalid literal for int() with base 10: 'tot_lvl'

#100 RieLuc23 opened 5 days ago
1
kreport2krona.py vs ktImportTaxonomy

#99 ChillarAnand closed 1 month ago
0
combine_kreports.py error

#98 sarrahroseml opened 3 months ago
0
sample and negative control

#97 nicolo-tellini opened 3 months ago
0
beta_diversity.py error

#96 Kamouyiaraki opened 4 months ago
0
no reads generated after running extract_kraken_reads.py

#95 caizhangbin opened 6 months ago
2
differences in report from kraken2 and make_kreport.py

#94 moxgreen opened 7 months ago
0
extract_kraken_reads.py not working when read mates have unique names

#93 RHaagmans opened 8 months ago
0
extract_kraken_reads.py accept bracken reports?

#92 Sabrin2020 opened 10 months ago
2
1_all vs 1_lvl

#91 mars188 opened 10 months ago
0
RuntimeError: generator raised StopIteration

#90 snehamurthy21 opened 11 months ago
0
"other entries", "other sequences" raise AttributeError when using --include-children

#89 yeemey opened 11 months ago
0
combine_kreports.py: Latest version missing unclassified reads for last sample

#88 sfredr closed 11 months ago
2
Merge in changes to account for kreport2mpa

#87 jenniferlu717 closed 1 year ago
0
Make_kreports.py breaks if all reads unclassified

#86 mattheatley opened 1 year ago
1
extract_kraken_reads.py returns different read counts for paired fastqs

#85 matbeale opened 1 year ago
2
Issue and fix for kreport2mpa.py script - domain misrepresented with "k" and taxon underscore flexibility

#84 jmboccacino closed 1 year ago
2
combining krakenuniq reports

#83 Sabrin2020 opened 1 year ago
2
Regarding output generated from beta_diversity command

#82 In2S closed 1 year ago
2
Including sample names in header of combine_mpa.py

#81 susheelbhanu closed 1 year ago
1
filter_bracken_output.py: Too many arguments in line

#80 bheimbu closed 1 year ago
2
Update alpha_diversity.py

#79 recepcanaltinbag opened 1 year ago
0
Should sequencing depth be considered？

#78 Yunliang81 opened 1 year ago
2
No kraken2_translate.py after downloading the KrakenTools?

#77 B-1991-ing opened 1 year ago
1
extract_kraken_reads.py does not keep base quality score

#76 BenjaminDelisle closed 1 year ago
2
combine_kreports -- AttributeError: 'int' object has no attribute 'level_num'

#75 douglas-hoen closed 1 year ago
3
Is it possible to filter the kraken.report or bracken.report?

#74 B-1991-ing opened 1 year ago
1
extract_kraken_reads with --exclude excluding multiple taxids

#73 Afu5956 opened 1 year ago
1
Error when using --include-children

#72 nblouin opened 1 year ago
2
Handle kreports with no root line

#71 schorlton opened 1 year ago
0
Support strain level

#70 alienzj opened 1 year ago
0
Support strain level

#69 alienzj closed 1 year ago
0
kreport2map.py and strain profile

#68 alienzj opened 1 year ago
0
I would like to check if I can run 'combine_kreports.py' on my Kraken2 reports?

#67 Olla10 closed 1 year ago
1
How can I combine kraken2 output/reports from different samples and convert them into one report using Kraken Tool script?

#66 Olla10 opened 1 year ago
0
fix wrong script name in readme

#65 YedilSerzhan opened 1 year ago
0
Is it possible to create a new *.kraken and *.kraken.report besides extract specific reads

#64 B-1991-ing opened 1 year ago
0
Running alpha diversity on combined bracken reports

#63 adixit213 opened 1 year ago
0
Latest commit of kraken2mpa.py broke the script due to code that was meant for extract_kraken_reads.py

#62 simonleandergrimm closed 1 year ago
1
extract_kraken_reads.py input error

#61 nunrath closed 1 year ago
0
--include-children functionality in filter_bracken.out.py

#60 joshuakirsch opened 1 year ago
0
Error running kreports2mpa.py

#59 ghost opened 1 year ago
3
Add biopython dependency to istallation instructions

#58 kim-fehl closed 1 year ago
1
error running kreport2mpa.py script, name 'l_vals' is not defined.

#57 Sautumn-Lin opened 1 year ago
8
Filtered Bracken-style output to Kraken reports format

#56 myshu2017-03-14 opened 1 year ago
2
extract reads error

#55 senukobla opened 1 year ago
1
error running kreport2mpa.py script

#54 hillms opened 1 year ago
4
Update README.md

#53 martin-steinegger opened 2 years ago
0
error with "combine_mpa.py" script when combining mpa report with header

#52 weiweiziyan opened 2 years ago
2
ADD: Script to allow metaphlan3 output generation

#51 damioresegun opened 2 years ago
0