hariszaf/pema

Issues

• Wrong sample names in OutputPerSample

  #69 opened 7 months ago by JustinePa
  5

• Long recurrent taxonomic labels

  #68 opened 9 months ago by stas-malavin
  1

• pandaseq error "Something is wrong with this ID"

  #67 opened 9 months ago by stas-malavin
  17

• Storage usage of PEMA

  #65 opened a year ago by savvas-paragkamian
  1

• Error PEMA ASV inference: Directory swarm does not exists

  #59 opened a year ago by savvas-paragkamian
  5

• time consuming preprocessing

  #63 opened a year ago by hariszaf
  0

• Needed updates on "PEMA's output files.md"

  #62 opened a year ago by JustinePa
  2

• When Swarm is chosen for the ITS, the names of the sequences are OtuXX and not ASVXX

  #61 opened a year ago by cpavloud
  4

• 16s copy number

  #60 opened a year ago by hariszaf
  0

• Unexpected Singletons in Final Table despite removeSingletons set to "Yes"

  #58 opened a year ago by JustinePa
  5

• PEMA to create a run summary file

  #55 opened 2 years ago by kmexter
  2

• NCBI Taxon ID included in the final_table.tsv file?

  #29 opened 3 years ago by cpavloud
  12

• Parameters file in a structured format

  #35 opened 3 years ago by hariszaf
  12

• Describe formally the pema output

  #38 opened 3 years ago by hariszaf
  2

• Enhancement: Add bbmap suite for read preprocessing

  #39 opened 3 years ago by natgiot
  1

• provide pema main data product in a 7-level taxonomy format

  #52 opened 2 years ago by hariszaf
  3

• extended final table

  #53 opened 2 years ago by kmexter
  1

• PEMA Ro-Crate

  #54 opened 2 years ago by kmexter
  1

• MIDORI updates

  #56 opened 2 years ago by kmexter
  2

• Add alternative ref db for the case of COI

  #20 opened 3 years ago by hariszaf
  1

• Consider incorporating tools for pseudogene detection

  #27 opened 3 years ago by cpavloud
  3

• Upgrade to crest4

  #51 opened 2 years ago by hariszaf
  0

• Option of running PEMA in distinct steps

  #43 opened 2 years ago by georgiatari
  2

• MAPseq alternative classifier for the case of rRNA genes

  #44 opened 2 years ago by hariszaf
  0

• custom_ref_db doesn't work.

  #50 opened 2 years ago by hyeiny119
  5

• add remove_singletons option in OTU pipeline

  #47 opened 2 years ago by natgiot
  4

• HPC job specifications

  #49 opened 2 years ago by marymcelroy
  4

• Error when unzipping using a checkpoing

  #48 opened 2 years ago by hariszaf
  1

• PEAR as merging algorithm in PEMA

  #42 opened 2 years ago by georgiatari
  1

• Enhancement: Add option for users to provide a custom adapter file

  #40 opened 3 years ago by natgiot
  1

• alternative database for COI marker gene

  #41 opened 3 years ago by hariszaf
  2

• Add new database for 16S/18S (SILVA 138)

  #26 opened 3 years ago by cpavloud
  1

• Species level missed in `finalTable.tsv`

  #36 opened 3 years ago by hariszaf
  0

• Data provenance considerations

  #28 opened 3 years ago by cpavloud
  6

• ITS sanity check fails

  #34 opened 3 years ago by probonas
  1

• Add 12S marker gene

  #32 opened 3 years ago by hariszaf
  3

• Add alternative db for the case of 18S rRNA

  #21 opened 3 years ago by hariszaf
  1

• PEMA dependencies

  #13 opened 3 years ago by deniskristak
  4

• PEMAbase needs to be indenpendent from any local files

  #31 opened 3 years ago by hariszaf
  4

• Empty 8.outputPerSample folder

  #25 opened 3 years ago by cpavloud
  3

• Fatal error: ./pema_latest.bds, line 446

  #10 opened 3 years ago by ElhamKarimi
  1

• Conversion to ENA format - Sample names

  #23 opened 3 years ago by cpavloud
  4

• Convert raw data from other than MiSeq sequencers to PEMA format

  #19 opened 3 years ago by hariszaf
  0

• Fail with 18S data and vsearch algorithm

  #22 opened 3 years ago by hariszaf
  3

• Fail with 18S data and swarm algorithm

  #24 opened 3 years ago by cpavloud
  1

• Getting an error about '16S_otutab.txt': No such file or directory with the example

  #2 opened 4 years ago by pradac
  1

• cannot remove 'nospace.*': No such file or directory

  #8 opened 4 years ago by Tclack88
  8

• why this Fatal error: /home/pema_latest.bds, line 175, pos 1. Task/s failed

  #6 opened 4 years ago by Akhilbiju01
  8

• Checkpoint not working

  #1 opened 5 years ago by jedlennox
  6