marcelm/cutadapt

Issues

• cutadapt: error: cutadapt not able to trim the desired adapto

  #785 opened a month ago by faizee-ali
  1

• Unexpected trimming behavior

  #784 opened a month ago by adrianomartinelli
  0

• "OverflowError: FASTA/FASTQ record does not fit into buffer" when trimming ONT reads

  #783 opened a month ago by diego-rt
  7

• Pipe multiple adatper trimming steps is unsupported when using the python API.

  #777 opened 2 months ago by y9c
  5

• Nanopore adapter detection

  #782 opened 2 months ago by Hedi65
  1

• FYI: Macos-14 runners available for M1 macs.

  #770 opened 3 months ago by rhpvorderman
  2

• Error: BiocParallel errors

  #779 opened 2 months ago by ThibauldMichel
  5

• Remove the "Incomplete adapter sequence" warning

  #780 opened 2 months ago by marcelm
  0

• Ensuring to find the correct file after Demultiplexing my 16S amplicon raw dataset with combinatorial dual indexes cutadapt command

  #776 opened 2 months ago by JayalalKJ
  5

• Cutadapt 4.7 hangs when using process substitution

  #772 opened 2 months ago by Redmar-van-den-Berg
  10

• Write a user guide specifically for ONT data

  #742 opened 6 months ago by rhpvorderman
  18

• Feature request: Support for multiple FastQ pairs

  #775 opened 2 months ago by Redmar-van-den-Berg
  0

• cutadapt cannot read from stdin with xopen 2.0.0

  #774 opened 2 months ago by peterjc
  3

• Crash on sending interleaved output to stdout

  #773 opened 3 months ago by marcelm
  0

• Reads not trimmed for PE with poly-G

  #771 opened 3 months ago by joegeorgeson
  5

• Installing via FreeBSD ports and pkgsrc

  #769 opened 3 months ago by outpaddling
  3

• Vectorize alignment algorithm for x86-64

  #768 opened 3 months ago by rhpvorderman
  0

• Cutadapt writes some errors to STDOUT instead of STDERR

  #767 opened 3 months ago by johanneskoester
  6

• Questions about trimming when both -g and -a options are present

  #766 opened 3 months ago by dbrg77
  3

• Need help in using cutadapt to trim paired-end fastq reads to provide as input for DADA2

  #765 opened 3 months ago by akspat
  4

• Output of demultiplexing mixed oriented reads

  #764 opened 3 months ago by luigallucci
  5

• Error in file.py, "OutStream" object does not have attribute 'buffer'

  #763 opened 4 months ago by karenyun
  3

• Use `--action=lowercase` for short reads but keep trimmed passed reads.

  #762 opened 4 months ago by y9c
  2

• Could not build wheels for cutadapt for mac 12.7.1 monterey

  #738 opened 4 months ago by Wardah0q
  1

• NextSeq Quality Trimming Issue

  #758 opened 4 months ago by gfill88
  3

• When demultiplexing, report contains irrelevant line

  #760 opened 4 months ago by marcelm
  0

• feature request: ubam support?

  #757 opened 5 months ago by eboyden
  4

• Make Cutadapt portable on macOS

  #756 opened 5 months ago by DmitriiSukhomlinov
  11

• sc/snATAC-seq barcode correction

  #754 opened 5 months ago by sknaack
  5

• ERROR: Error in sequence file at unknown line: Reads are improperly paired

  #755 opened 5 months ago by starz77
  2

• Installation instructions need conda channel

  #752 opened 5 months ago by susheelbhanu
  2

• poly-A trimming for paired-end data - consider orientation

  #753 opened 5 months ago by benemead
  2

• Question about the paired-end read trimming.

  #751 opened 5 months ago by chaibenl
  1

• KmerFinder: x of length y is longer than the maximum of 64

  #749 opened 6 months ago by marcelm
  1

• Feature request: ONT Chimeric read splitting

  #747 opened 6 months ago by rhpvorderman
  1

• paired fasta input with multiple cores

  #746 opened 6 months ago by bernt-matthias
  7

• How to handle reads with alternative adapters or primer sequences

  #744 opened 6 months ago by fxfish
  4

• ModuleNotFoundError: No module named 'cutadapt.cli'

  #735 opened 6 months ago by Chloelyc
  1

• Catching ONT adapters: allow setting insertion and deletion scores

  #745 opened 6 months ago by rhpvorderman
  4

• Small ONT optimization: length filtering before applying trimming

  #743 opened 6 months ago by rhpvorderman
  1

• Add Reverse Complement modification function.

  #737 opened 7 months ago by galaxy001
  3

• cutadapt pair-adapters almost all sequences end up in the unknown fastq files

  #741 opened 7 months ago by cpavloud
  11

• Add --trimmed-poly-a-only for poly-a as --trimmed-only for adapter

  #740 opened 7 months ago by a92932000
  0

• why the 5' adapter wasn't trimmed when adding --revcomp.

  #739 opened 7 months ago by permia
  2

• UMI '--rename' regex/utility

  #736 opened 8 months ago by joegeorgeson
  1

• Collisions in the adapter index should be handled more gracefully

  #734 opened 8 months ago by marcelm
  0

• Option `--rename` only works in single thread mode

  #732 opened 8 months ago by pontushojer
  1

• Keep UMI after adapter sequence?

  #729 opened 8 months ago by jamesboot
  3

• kmer_finder test failing in architecture i386

  #730 opened 8 months ago by linqigang888
  5

• Demultiplexing favors the first barcode given?!

  #724 opened 9 months ago by fesel2
  5