jenniferlu717/Bracken

Issues

• Lower nr of reads at Class compared to Order level Bracken

  #257 opened 2 months ago by CETHuyghe
  1

• Minimizer counts column in bracken report

  #211 opened a year ago by mlarjim
  1

• Is it possible to specify multiple databases for classification？

  #263 opened a month ago by smoothyly
  0

• est_abundance.py, ValueError: '1' is not in list

  #227 opened 10 months ago by ChathumadaviE
  8

• Question: Would it be possible to concatenate the braken read assignments from 2 different databases (1 bacterial database & 1 viral database)?

  #250 opened a month ago by the-eon-flux
  2

• Segmentation fault when trying to build krakenuniq database

  #262 opened a month ago by jalalsiddiqui
  0

• Bracken read length for ITS1 amplicons

  #260 opened 2 months ago by ARW-UBT
  1

• Question about calculations and intersample comparison

  #259 opened 2 months ago by alanxelena
  1

• Install failed: chmod: cannot access \u2018bracken-build\u2019: No such file or directory

  #261 opened 2 months ago by YutongLi5276
  0

• seqid2taxid can't find seqid

  #258 opened 2 months ago by eric9n
  0

• Segmentation Fault - Core Dumped Issue (Step 3 - Converting Kmer Mappings into Read Classifications)

  #255 opened 2 months ago by ulin27
  0

• bracken 2.9 build error

  #253 opened 2 months ago by 0russ4
  1

• bracken-build: line 229: syntax error: unexpected end of file error

  #254 opened 2 months ago by balaram26
  1

• bracken-build - syntax error: unexpected end of file

  #252 opened 3 months ago by nicholascdove
  3

• bracken is not working with kraken2

  #251 opened 3 months ago by lyisrae1
  1

• Strange Bracken results indicating Brassica Rapa reads in the Human RNASeq COVID Samples

  #243 opened 5 months ago by Rohit-Satyam
  4

• Wrong docs for https://benlangmead.github.io/aws-indexes/k2 prebuilt DBs

  #249 opened 3 months ago by paulzierep
  1

• Should the kmer length of bracken always have the same length of the used kraken2 DB ?

  #248 opened 3 months ago by paulzierep
  3

• krakenuniq not working due fix-commit after release

  #247 opened 3 months ago by pustoshilov-d
  1

• Extract certain reads belonging to certain taxa.

  #246 opened 4 months ago by luzhang321
  1

• /

  #244 opened 4 months ago by CETHuyghe
  0

• S1 level re-estimation doesn't seem to work for us

  #242 opened 6 months ago by swelbo
  4

• what kmer size should be used for paired end read data?

  #234 opened 6 months ago by gregcaporaso
  2

• Convert bracken output to mpa file

  #241 opened 7 months ago by snehamurthy21
  0

• Choosing read length for Oxford Nanopore long reads

  #240 opened 7 months ago by andreyeremin
  0

• Reads being redistributed to lower abundance species over higher abundance species within the Bacillus genus

  #233 opened 8 months ago by nphage
  3

• bracken-build syntax error

  #232 opened 9 months ago by ythuangmyco
  2

• bracken-build runs out of memory while kraken2 does not

  #235 opened 9 months ago by NikolasVellnow
  1

• Error running Nat Protoc example data

  #238 opened 8 months ago by ellisjj
  1

• threshold as percent/fraction rather than read number

  #239 opened 9 months ago by rjsorr
  0

• Counts at species level don't sum to root

  #237 opened 9 months ago by sconlan
  1

• low complexity plant samples are completely masked "xxxxx" and use up a lot of memory

  #236 opened 9 months ago by mclaugsf
  0

• Bracken greatly inflating total bacterial reads

  #226 opened 10 months ago by jpmcelderry
  4

• Report the most precise level

  #229 opened 10 months ago by steven-bioinfo
  0

• bracken v2.8 from both release taged v2.8 and conda/mamba does no support for krakenuniq but source code of git do

  #228 opened 10 months ago by lvzenglei
  1

• est_abundance.py error

  #230 opened 9 months ago by ojbednar
  1

• Dict_keys not subscriptable error with combine_bracken_outputs.py

  #221 opened a year ago by namon1994
  1

• Incorrect reassignments of kraken2 reads with bracken

  #225 opened a year ago by rmcolq
  0

• Inquiry about the Discrepancy in Classification Results between Kraken2 and Bracken for Gut Metagenomic Data

  #224 opened a year ago by Tonny-zhou
  0

• can bracken estimate abundance on different level one time?

  #223 opened a year ago by MGI-tech-bioinformatics
  0

• Why does bracketen delete bacteria in kraken2？

  #222 opened a year ago by Xuanpei-Zhai
  0

• kmer2read_distr puts invalid taxids in database*mers.kraken file

  #220 opened a year ago by rrwick
  0

• Kraken database b does not exist

  #219 opened a year ago by stefanielager
  2

• Syntax Error

  #217 opened a year ago by JochenSchaefergmxde
  1

• Classification issues with similar taxonomic ids

  #209 opened a year ago by jkimsis
  2

• Dealing with unclassified reads when calculating relative abundance

  #218 opened a year ago by andressamv
  0

• Typo in the name of executable script

  #216 opened a year ago by asan-emirsaleh
  0

• bracken giving no reads as an error constantly

  #215 opened a year ago by suvekshya21
  1

• Taxonomy IDs not matching for species Xylophagaidae: (92613 183505)

  #214 opened a year ago by B-1991-ing
  0

• Is there a way to get per-read taxonomy classification running Bracken?

  #213 opened a year ago by mclaugsf
  0