jenniferlu717/KrakenTools

Issues

• IndexError: string index out of range when using extract_kraken_reads

  #101 opened 6 days ago by fetyj
  4

• Construct a phylogenetic tree from Kraken2 in order to use in phyloseq object

  #46 opened 3 years ago by magibc
  10

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

  #100 opened 2 months ago by RieLuc23
  1

• kreport2krona.py not count the reads of bracken.Kreport

  #44 opened 3 years ago by gracielad
  2

• kreport2krona.py vs ktImportTaxonomy

  #99 opened 4 months ago by ChillarAnand
  0

• combine_kreports.py error

  #98 opened 6 months ago by sarrahroseml
  0

• extract_kraken_reads.py accept bracken reports?

  #92 opened a year ago by Sabrin2020
  2

• sample and negative control

  #97 opened 6 months ago by nicolo-tellini
  0

• beta_diversity.py error

  #96 opened 6 months ago by Kamouyiaraki
  0

• no reads generated after running extract_kraken_reads.py

  #95 opened 8 months ago by caizhangbin
  2

• Filtered Bracken-style output to Kraken reports format

  #56 opened 2 years ago by myshu2017-03-14
  2

• combining krakenuniq reports

  #83 opened a year ago by Sabrin2020
  2

• differences in report from kraken2 and make_kreport.py

  #94 opened 10 months ago by moxgreen
  0

• extract_kraken_reads.py not working when read mates have unique names

  #93 opened 10 months ago by RHaagmans
  0

• Should sequencing depth be considered？

  #78 opened 2 years ago by Yunliang81
  2

• 1_all vs 1_lvl

  #91 opened a year ago by mars188
  0

• RuntimeError: generator raised StopIteration

  #90 opened a year ago by snehamurthy21
  0

• "other entries", "other sequences" raise AttributeError when using --include-children

  #89 opened a year ago by yeemey
  0

• Error when using --include-children

  #72 opened 2 years ago by nblouin
  2

• Is it possible to filter the kraken.report or bracken.report?

  #74 opened 2 years ago by B-1991-ing
  1

• combine_kreports.py: Latest version missing unclassified reads for last sample

  #88 opened a year ago by sfredr
  2

• combine_kreports -- AttributeError: 'int' object has no attribute 'level_num'

  #75 opened a year ago by douglas-hoen
  3

• Regarding output generated from beta_diversity command

  #82 opened a year ago by In2S
  2

• extract_kraken_reads.py returns different read counts for paired fastqs

  #85 opened a year ago by matbeale
  2

• Add biopython dependency to istallation instructions

  #58 opened a year ago by kim-fehl
  1

• No kraken2_translate.py after downloading the KrakenTools?

  #77 opened 2 years ago by B-1991-ing
  1

• filter_bracken_output.py: Too many arguments in line

  #80 opened a year ago by bheimbu
  2

• Issue and fix for kreport2mpa.py script - domain misrepresented with "k" and taxon underscore flexibility

  #84 opened a year ago by jmboccacino
  2

• Make_kreports.py breaks if all reads unclassified

  #86 opened a year ago by mattheatley
  1

• Including sample names in header of combine_mpa.py

  #81 opened a year ago by susheelbhanu
  1

• extract_kraken_reads.py does not keep base quality score

  #76 opened 2 years ago by BenjaminDelisle
  2

• extract_kraken_reads with --exclude excluding multiple taxids

  #73 opened 2 years ago by Afu5956
  1

• error running kreport2mpa.py script

  #54 opened 2 years ago by hillms
  4

• kreport2map.py and strain profile

  #68 opened 2 years ago by alienzj
  0

• I would like to check if I can run 'combine_kreports.py' on my Kraken2 reports?

  #67 opened 2 years ago by Olla10
  1

• Latest commit of kraken2mpa.py broke the script due to code that was meant for extract_kraken_reads.py

  #62 opened 2 years ago by simonleandergrimm
  1

• How can I combine kraken2 output/reports from different samples and convert them into one report using Kraken Tool script?

  #66 opened 2 years ago by Olla10
  0

• Is it possible to create a new *.kraken and *.kraken.report besides extract specific reads

  #64 opened 2 years ago by B-1991-ing
  0

• error running kreport2mpa.py script, name 'l_vals' is not defined.

  #57 opened 2 years ago by Sautumn-Lin
  8

• Running alpha diversity on combined bracken reports

  #63 opened 2 years ago by adixit213
  0

• Error running kreports2mpa.py

  #59 opened 2 years ago by Platelmin1o
  3

• extract_kraken_reads.py input error

  #61 opened 2 years ago by nunrath
  0

• --include-children functionality in filter_bracken.out.py

  #60 opened 2 years ago by joshuakirsch
  0

• error with "combine_mpa.py" script when combining mpa report with header

  #52 opened 2 years ago by weiweiziyan
  2

• extract reads error

  #55 opened 2 years ago by senukobla
  1

• extract kraken read _empty fastq file

  #47 opened 3 years ago by arz19893
  1

• Metaphlan3 integration for kreport2mpa

  #50 opened 2 years ago by damioresegun
  1

• behaviour of extract_kraken_reads

  #48 opened 3 years ago by jorondo1
  0

• Matching many tax ids

  #45 opened 3 years ago by dnolin13
  0

• Unable to download the kraken database?

  #43 opened 3 years ago by mathavanpu
  0