marcelm/cutadapt issues and pull requests

#806 - [Question] linked adapters from Fasta file and discarding untrimmed pairs

Issue - State: open - Opened by marchoeppner 5 months ago - 1 comment

#805 - Suggestion: filter mode for polyA

Issue - State: open - Opened by NickNCL 5 months ago - 2 comments

#804 - Report.py raise error when `eranges` is None

Issue - State: open - Opened by y9c 5 months ago

#803 - Fix bug in report.py when dealing with empty list

Pull Request - State: open - Opened by y9c 5 months ago - 1 comment

#802 - Update bioconda-recipe to support osx-arm64

Issue - State: closed - Opened by isaacovercast 5 months ago - 2 comments

#801 - cutadapt not recognizing second input file

Issue - State: closed - Opened by izabelstohel 5 months ago - 1 comment

#800 - Unable to trim primers from my interleaved fastq files

Issue - State: open - Opened by kdbchau 5 months ago - 4 comments

#799 - Should I use -a or -g when demultiplexing ONT reads with dual barcodes?

Issue - State: open - Opened by ashleyp1 5 months ago - 3 comments

#798 - Primer sequence trimming. Cutadapt does not cut all of them

Issue - State: open - Opened by Guillermouceda 5 months ago - 1 comment

#797 - -m don't correctly work for pair-end analysis

Issue - State: closed - Opened by Flying-Doggy 6 months ago - 1 comment

#796 - Simplify expected errors function

Pull Request - State: open - Opened by rhpvorderman 6 months ago - 1 comment

#795 - Issue importing fasta files to Cutadapt virtual environment

Issue - State: open - Opened by elkst00 6 months ago - 1 comment

#794 - Using --revcomb on paired-end data

Issue - State: open - Opened by ThomePauline 6 months ago - 1 comment

#793 - Update cli.py

Pull Request - State: open - Opened by MaWeffm 6 months ago - 2 comments

#792 - Heterogeneity Spacers and Primers

Issue - State: open - Opened by luigallucci 7 months ago - 2 comments

#791 - Problems reading stdin on Windows 11 Python 3.12

Issue - State: open - Opened by peterjc 7 months ago - 5 comments

#790 - Adapters in form of file and linked mode

Issue - State: closed - Opened by luigallucci 7 months ago - 4 comments

#789 - Help to get accurate counts of demultiplexed amplicons using cutadapt

Issue - State: closed - Opened by bgpalmer 7 months ago - 2 comments

#788 - Feature request: shorten paired-end reads with separate values for --length

Issue - State: closed - Opened by MaWeffm 8 months ago - 1 comment

#787 - Adapter matches in the middle of a read masked with N

Issue - State: open - Opened by hmutpw 8 months ago - 2 comments

#786 - Error in FASTQ file at line 20136: Length of sequence and qualities differ

Issue - State: closed - Opened by Missthepast 8 months ago - 2 comments

#785 - cutadapt: error: cutadapt not able to trim the desired adapto

Issue - State: open - Opened by faizee-ali 8 months ago - 3 comments

#784 - Unexpected trimming behavior

Issue - State: closed - Opened by adrianomartinelli 9 months ago - 5 comments

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

Issue - State: open - Opened by diego-rt 9 months ago - 7 comments

#782 - Nanopore adapter detection

Issue - State: closed - Opened by Hedi65 9 months ago - 1 comment

#781 - Allow multiple AdapterCutters and ReverseComplementers in a pipeline

Pull Request - State: closed - Opened by marcelm 9 months ago - 1 comment

#780 - Remove the "Incomplete adapter sequence" warning

Issue - State: open - Opened by marcelm 9 months ago

#779 - Error: BiocParallel errors

Issue - State: closed - Opened by ThibauldMichel 9 months ago - 5 comments

#778 - Update report.py to fix the error in API

Pull Request - State: closed - Opened by y9c 9 months ago - 2 comments

#777 - Pipe multiple adatper trimming steps is unsupported when using the python API.

Issue - State: closed - Opened by y9c 9 months ago - 5 comments

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

Issue - State: open - Opened by JayalalKJ 9 months ago - 5 comments

#775 - Feature request: Support for multiple FastQ pairs

Issue - State: open - Opened by Redmar-van-den-Berg 10 months ago

#774 - cutadapt cannot read from stdin with xopen 2.0.0

Issue - State: closed - Opened by peterjc 10 months ago - 3 comments

#773 - Crash on sending interleaved output to stdout

Issue - State: closed - Opened by marcelm 10 months ago

#772 - Cutadapt 4.7 hangs when using process substitution

Issue - State: closed - Opened by Redmar-van-den-Berg 10 months ago - 10 comments

#771 - Reads not trimmed for PE with poly-G

Issue - State: closed - Opened by joegeorgeson 10 months ago - 5 comments

#770 - FYI: Macos-14 runners available for M1 macs.

Issue - State: closed - Opened by rhpvorderman 10 months ago - 2 comments

#769 - Installing via FreeBSD ports and pkgsrc

Issue - State: closed - Opened by outpaddling 10 months ago - 3 comments

#768 - Vectorize alignment algorithm for x86-64

Issue - State: open - Opened by rhpvorderman 10 months ago - 1 comment

#767 - Cutadapt writes some errors to STDOUT instead of STDERR

Issue - State: closed - Opened by johanneskoester 10 months ago - 6 comments

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

Issue - State: closed - Opened by dbrg77 10 months ago - 3 comments

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

Issue - State: closed - Opened by akspat 11 months ago - 4 comments

#764 - Output of demultiplexing mixed oriented reads

Issue - State: open - Opened by luisymbio 11 months ago - 5 comments

#763 - Error in file.py, "OutStream" object does not have attribute 'buffer'

Issue - State: closed - Opened by karenyun 11 months ago - 3 comments

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

Issue - State: closed - Opened by y9c 12 months ago - 2 comments
Labels: API

#761 - Remote File Support for input files

Pull Request - State: open - Opened by geertvandeweyer 12 months ago - 5 comments

#760 - When demultiplexing, report contains irrelevant line

Issue - State: open - Opened by marcelm 12 months ago

#759 - Add admonition about info-file w/r/t paired end mode

Pull Request - State: closed - Opened by odoublewen 12 months ago - 1 comment

#758 - NextSeq Quality Trimming Issue

Issue - State: closed - Opened by gfill88 12 months ago - 3 comments

#757 - feature request: ubam support?

Issue - State: open - Opened by eboyden 12 months ago - 4 comments

#756 - Make Cutadapt portable on macOS

Issue - State: closed - Opened by DmitriiSukhomlinov about 1 year ago - 11 comments

#755 - ERROR: Error in sequence file at unknown line: Reads are improperly paired

Issue - State: closed - Opened by starz77 about 1 year ago - 2 comments

#754 - sc/snATAC-seq barcode correction

Issue - State: open - Opened by sknaack about 1 year ago - 5 comments

#753 - poly-A trimming for paired-end data - consider orientation

Issue - State: open - Opened by benemead about 1 year ago - 2 comments

#752 - Installation instructions need conda channel

Issue - State: closed - Opened by susheelbhanu about 1 year ago - 2 comments

#751 - Question about the paired-end read trimming.

Issue - State: open - Opened by chaibenl about 1 year ago - 1 comment

#750 - Fix issue with long adapters for kmer finder

Pull Request - State: closed - Opened by rhpvorderman about 1 year ago - 1 comment

#749 - KmerFinder: x of length y is longer than the maximum of 64

Issue - State: closed - Opened by marcelm about 1 year ago - 1 comment

#748 - Follow best practices for pointer aliasing in alignment inner loop.

Pull Request - State: closed - Opened by rhpvorderman about 1 year ago - 3 comments

#747 - Feature request: ONT Chimeric read splitting

Issue - State: open - Opened by rhpvorderman about 1 year ago - 1 comment

#746 - paired fasta input with multiple cores

Issue - State: closed - Opened by bernt-matthias about 1 year ago - 7 comments

#744 - How to handle reads with alternative adapters or primer sequences

Issue - State: closed - Opened by fxfish about 1 year ago - 4 comments

#743 - Small ONT optimization: length filtering before applying trimming

Issue - State: open - Opened by rhpvorderman about 1 year ago

#742 - Write a user guide specifically for ONT data

Issue - State: open - Opened by rhpvorderman about 1 year ago - 18 comments

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

Issue - State: closed - Opened by cpavloud about 1 year ago - 11 comments

#740 - Add --trimmed-poly-a-only for poly-a as --trimmed-only for adapter

Issue - State: open - Opened by a92932000 about 1 year ago

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

Issue - State: closed - Opened by permia about 1 year ago - 2 comments

#738 - Could not build wheels for cutadapt for mac 12.7.1 monterey

Issue - State: closed - Opened by Wardah0q about 1 year ago - 1 comment

#737 - Add Reverse Complement modification function.

Issue - State: open - Opened by galaxy001 about 1 year ago - 3 comments

#736 - UMI '--rename' regex/utility

Issue - State: open - Opened by joegeorgeson about 1 year ago - 1 comment
Labels: feature-request

#735 - ModuleNotFoundError: No module named 'cutadapt.cli'

Issue - State: closed - Opened by Chloelyc over 1 year ago - 1 comment

#734 - Collisions in the adapter index should be handled more gracefully

Issue - State: closed - Opened by marcelm over 1 year ago

#733 - Add sphinx-rtd-theme

Pull Request - State: closed - Opened by marcelm over 1 year ago

#732 - Option `--rename` only works in single thread mode

Issue - State: closed - Opened by pontushojer over 1 year ago - 1 comment

#731 - Update _kmer_finder.pyx to always use a 64-bit integer.

Pull Request - State: closed - Opened by rhpvorderman over 1 year ago - 4 comments

#730 - kmer_finder test failing in architecture i386

Issue - State: closed - Opened by linqigang888 over 1 year ago - 5 comments

#729 - Keep UMI after adapter sequence?

Issue - State: closed - Opened by jamesboot over 1 year ago - 3 comments

#728 - Attempt to fix the sphinx theme

Pull Request - State: closed - Opened by marcelm over 1 year ago

#727 - Make expected errors use doubles again for increased precision

Pull Request - State: closed - Opened by rhpvorderman over 1 year ago - 5 comments

#726 - Speed up expected errors calculations using SSE2 instructions

Pull Request - State: closed - Opened by rhpvorderman over 1 year ago - 7 comments

#725 - Add an option for maximum average error rate (--max-aer)

Pull Request - State: closed - Opened by rhpvorderman over 1 year ago - 7 comments

#724 - Demultiplexing favors the first barcode given?!

Issue - State: closed - Opened by fesel2 over 1 year ago - 5 comments

#723 - Trouble removing RevComp reads in the FWD.ForwardReads orientation and Forward reads in the FWD.ReverseReads orientation

Issue - State: closed - Opened by pennelli19 over 1 year ago - 3 comments

#722 - Clarification of "Reads that were too long"

Issue - State: closed - Opened by HenriettaHolze over 1 year ago - 2 comments

GitHub / marcelm/cutadapt issues and pull requests