qiime2/q2-dada2

Issues

• Throw an error when 1 sample is provided

  #170 opened 22 days ago by colinbrislawn
  2

• Add warning when pooling method and chimera detection method are misaligned

  #165 opened 6 months ago by benjjneb
  1

• BUG:Can not run qiime dada2 denoise-ccs without primers or adapters

  #163 opened a year ago by cherman2
  6

• ENH: include error model plots in denoise-* output

  #158 opened 2 years ago by nbokulich
  3

• dada2 justConcatenate

  #129 opened 5 years ago by ARW-UBT
  6

• dada2 drops samples without reads unfiltered reads from table but not denoising stats.

  #136 opened 4 years ago by dwthomas
  1

• Error in sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))

  #119 opened a year ago by Preve92
  13

• Add pooling options to Q2 workflows

  #87 opened a year ago by benjjneb
  8

• Importing DADA2 R rep. sequences into QIIME2

  #159 opened 2 years ago by dixi06
  1

• Add long-read support

  #101 opened 2 years ago by benjjneb
  27

• Certain ID schemes can become mixed up with barcodes during sorting

  #102 opened 2 years ago by ebolyen
  3

• Restructuring dada2 R/python code

  #147 opened 2 years ago by jordenrabasco
  0

• error while using dada2 in qiime2

  #150 opened 2 years ago by NainaK6
  1

• expose minOverlap parameter

  #117 opened 4 years ago by nbokulich
  10

• Update to latest DADA2 for R 4.0 support

  #133 opened 4 years ago by ebolyen
  1

• Improved error reporting for malformed paired-end reads

  #97 opened 7 years ago by ConstantinoSchillebeeckx
  0

• denoise-paired: add flag for just concatenating paired reads

  #93 opened 7 years ago by AstrobioMike
  0

• denoise-*: expose `--collapse-no-mismatch` parameter

  #92 opened 7 years ago by nbokulich
  10

• Add an explicit error for return code -9

  #86 opened 7 years ago by ebolyen
  4

• Split filtering into its own command?

  #51 opened 8 years ago by benjjneb
  7

• Update denoise-paired document from minimum overlap 20 > 12nt

  #123 opened 5 years ago by mestaki
  0

• Setting "allowOneOf" and "maxMismatch" parameters in q2/dada2 plugin

  #126 opened 5 years ago by francis29029
  1

• Improve summary for merging paired reads

  #98 opened 6 years ago by antgonza
  4

• denoise-paired: add % merged to stats output

  #115 opened 5 years ago by nbokulich
  0

• denoise-paired: expose matchIDs parameter

  #118 opened 5 years ago by colinbrislawn
  3

• Upgrade to DADA2 >= 1.7.3

  #85 opened 6 years ago by thermokarst
  21

• I've gone through tutorials and forums and still don't understand how to select the truncLen and trim parameters in dada2

  #114 opened 6 years ago by milenapi
  1

• expose minimum-length parameter?

  #72 opened 6 years ago by jairideout
  5

• Allow denoise-single to process either reverse or forward reads

  #100 opened 6 years ago by mestaki
  3

• Add more DADA2 parameters to the wrapper

  #99 opened 6 years ago by apcamargo
  3

• Upgrading to 2017.12 breaks `q2-dada2`/`dada2`

  #84 opened 6 years ago by jakereps
  8

• Create report visualizer

  #79 opened 7 years ago by thermokarst
  6

• A workaround for q2-dada2 and a local R installation with dada2

  #68 opened 7 years ago by ebolyen
  9

• Add citations

  #94 opened 7 years ago by ebolyen
  0

• adding 454/ion torrent support

  #76 opened 7 years ago by gregcaporaso
  2

• Error in isBimeraDenovoTable(unqs[[i]], ..., verbose = verbose) : Input must be a valid sequence table.

  #90 opened 7 years ago by bassio
  1

• Turning chimera checking off breaks the plugin

  #88 opened 7 years ago by benjjneb
  1

• Segfault errors in 2017.12 plugin version

  #80 opened 7 years ago by benjjneb
  13

• conda installed dada2 is slow

  #74 opened 7 years ago by benjjneb
  19

• Report number or fraction of reads that pass each step

  #77 opened 7 years ago by benjjneb
  12

• Error bubbling or better error documentation

  #69 opened 7 years ago by maxvonhippel
  19

• trunc_len=0 can't be used

  #67 opened 7 years ago by gregcaporaso
  1

• Add support for variable amplicon lengths

  #64 opened 7 years ago by benjjneb
  1

• Add truncLen requirements to the denoise-paired help text

  #52 opened 7 years ago by benjjneb
  1

• Use DADA2 1.4 to fix quality-score precedence bug in parameters

  #56 opened 7 years ago by ebolyen
  2

• Update plugin to 1.4.0 R package

  #57 opened 7 years ago by benjjneb
  0

• delete `plot-qualities` visualizer in favor of `qiime demux summarize`

  #59 opened 7 years ago by gregcaporaso
  0

• Add chimera filtering options

  #50 opened 7 years ago by benjjneb
  3

• resolve potential bug related to missing filtered samples

  #49 opened 8 years ago by jairideout
  1

• qiime dada2 denoise-paired open up options for percent mismatch and overlap length

  #48 opened 8 years ago by shiffer1
  12