usadellab/Trimmomatic

Issues

• closed

  #69 opened 3 months ago by mennth01
  0

• ILLUMINACLIP: Unknown Trimmer

  #57 opened a year ago by RankAma
  1

• Differences in trimming between Novaseq and Nextseq outputs

  #68 opened 4 months ago by peterashtonEMHP
  0

• Installing

  #66 opened 6 months ago by lynneitelson
  0

• False positive：java.io.FileNotFoundException: /tools/Trimmomatic-0.39/adapters.fa (No such file or directory)

  #65 opened 7 months ago by Warelock
  0

• Not executable - Reg.

  #64 opened 7 months ago by bioramg
  1

• Building on Ubuntu 20

  #24 opened 3 years ago by chababster
  3

• Nextera Adapters sequences.

  #63 opened 9 months ago by Kauthar-Omar
  0

• Potential add on to Log File

  #62 opened 9 months ago by AAA-3
  0

• Error in tempfile()

  #61 opened 10 months ago by tdyoshida
  0

• What's the function of "-validatePairs"?

  #60 opened a year ago by Siteng999
  0

• Foward only surviving reads but no reverse only surviving and no dropped reads

  #56 opened a year ago by Catv97
  2

• What is the extra 1 base in the Truseq adapter file (TruSeq3-PE-2.fa)

  #58 opened a year ago by wjlim
  0

• Universal adapter

  #54 opened a year ago by zivlang
  0

• Error: Exception in thread "main" java.io.IOException: Stale file handle

  #49 opened 2 years ago by FelipeMSD
  2

• installation manual needed

  #53 opened a year ago by konopinski
  1

• question about ILLUMINACLIP 2:30:10

  #52 opened a year ago by scmicrosys
  0

• Trimmomatic drops 50% of reads

  #51 opened a year ago by RacheliHadjez
  0

• In what scenarios would you recommend using the SLIDINGWINDOW vs. MAXINFO modes?

  #22 opened 3 years ago by lucygarner
  1

• Making a custom adapter file - confused about the sequences to include

  #20 opened 3 years ago by lucygarner
  9

• intallation 0.40

  #48 opened 2 years ago by DavidGO464
  3

• Question about dealing with 10x data on trimmomatic

  #47 opened 2 years ago by mat10d
  0

• Trimmomatic parallel de/compression

  #46 opened 2 years ago by fgvieira
  0

• if the adapter.fa is needed and when to set keepbothreads TRUE

  #45 opened 2 years ago by taryl
  0

• Negative Value of "Input Read Pairs" and "Both Surviving" in log file

  #44 opened 2 years ago by lxwgcool
  2

• Quality score autodetection fails for Element Biosciences AVITI data

  #42 opened 2 years ago by michellescribner
  1

• 2nd paired fastq is empty

  #43 opened 2 years ago by dmncyap
  0

• paired read assignation

  #41 opened 2 years ago by PavelEG
  0

• Run time error exception occur

  #40 opened 2 years ago by GUNAJIV
  0

• Overrepresented sequences remain after adapter trimming

  #39 opened 2 years ago by judy-m2
  0

• Trimmomatic for MGIseq

  #38 opened 2 years ago by SergeyBaikal
  0

• Suggestion of updates to the README.md

  #37 opened 2 years ago by nicolasDelhomme
  0

• Build issue with JAVA Version

  #35 opened 2 years ago by bevsxyz
  1

• Trimmomatic not exiting after job finishes

  #34 opened 2 years ago by jesseaiton
  0

• Multiple Threads

  #33 opened 2 years ago by jesseaiton
  0

• Feature request: exit if adapter file is missing

  #31 opened 3 years ago by jdwinkler-lanzatech
  0

• Support for auto-detect the adapter sequence

  #30 opened 3 years ago by gaow
  0

• No survival & Incorrect input reads

  #29 opened 3 years ago by veedeeve
  0

• Inconsistency between design and implementation caused by misconception about ListIterator's previous() method

  #28 opened 3 years ago by zhangzhen
  2

• trimmomatic does not analyse all fastqs

  #27 opened 3 years ago by nana-marinbio
  1

• trimmomatic does not find adapters folder in coda env

  #26 opened 3 years ago by nana-marinbio
  1

• STDOUT appears to go to STDERR destination

  #25 opened 3 years ago by Ghepardo
  0

• still have N after trimming

  #23 opened 3 years ago by silinzhong
  0

• Trimmomatic errors

  #18 opened 3 years ago by Evansd36
  1

• encouding error on WSL

  #19 opened 3 years ago by XiudingCai
  1

• how to compile the source code?

  #17 opened 3 years ago by zhq90
  3

• keepBothReads - should it be "true" or "True"

  #21 opened 3 years ago by lucygarner
  1

• trimmomatic V0.39, keepBothReads: flag or boolean?

  #16 opened 3 years ago by TeiturAK
  2

• Specifying Adapter

  #14 opened 3 years ago by sci345
  1

• >90% forward surviving read pairs

  #15 opened 3 years ago by hcph
  2