marcelm cutadapt issues

marcelm / cutadapt

Cutadapt removes adapter sequences from sequencing reads

https://cutadapt.readthedocs.io

MIT License

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issues

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Problems reading stdin on Windows 11 Python 3.12

#791 peterjc opened 1 week ago
4
Adapters in form of file and linked mode

#790 luigallucci closed 1 week ago
4
Help to get accurate counts of demultiplexed amplicons using cutadapt

#789 bgpalmer closed 1 week ago
2
Feature request: shorten paired-end reads with separate values for --length

#788 MaWeffm closed 1 week ago
1
Adapter matches in the middle of a read masked with N

#787 hmutpw opened 1 month ago
2
Error in FASTQ file at line 20136: Length of sequence and qualities differ

#786 Missthepast closed 1 month ago
2
cutadapt: error: cutadapt not able to trim the desired adapto

#785 faizee-ali opened 1 month ago
3
Unexpected trimming behavior

#784 adrianomartinelli closed 1 month ago
5
"OverflowError: FASTA/FASTQ record does not fit into buffer" when trimming ONT reads

#783 diego-rt opened 1 month ago
7
Nanopore adapter detection

#782 Hedi65 closed 2 months ago
1
Allow multiple AdapterCutters and ReverseComplementers in a pipeline

#781 marcelm closed 2 months ago
1
Remove the "Incomplete adapter sequence" warning

#780 marcelm opened 2 months ago
0
Error: BiocParallel errors

#779 ThibauldMichel closed 2 months ago
5
Update report.py to fix the error in API

#778 y9c closed 2 months ago
2
Pipe multiple adatper trimming steps is unsupported when using the python API.

#777 y9c closed 2 months ago
5
Ensuring to find the correct file after Demultiplexing my 16S amplicon raw dataset with combinatorial dual indexes cutadapt command

#776 JayalalKJ opened 2 months ago
5
Feature request: Support for multiple FastQ pairs

#775 Redmar-van-den-Berg opened 3 months ago
0
cutadapt cannot read from stdin with xopen 2.0.0

#774 peterjc closed 3 months ago
3
Crash on sending interleaved output to stdout

#773 marcelm closed 3 months ago
0
Cutadapt 4.7 hangs when using process substitution

#772 Redmar-van-den-Berg closed 2 months ago
10
Reads not trimmed for PE with poly-G

#771 joegeorgeson closed 3 months ago
5
FYI: Macos-14 runners available for M1 macs.

#770 rhpvorderman closed 1 week ago
2
Installing via FreeBSD ports and pkgsrc

#769 outpaddling closed 3 months ago
3
Vectorize alignment algorithm for x86-64

#768 rhpvorderman opened 3 months ago
1
Cutadapt writes some errors to STDOUT instead of STDERR

#767 johanneskoester closed 3 months ago
6
Questions about trimming when both -g and -a options are present

#766 dbrg77 closed 3 months ago
3
Need help in using cutadapt to trim paired-end fastq reads to provide as input for DADA2

#765 akspat closed 3 months ago
4
Output of demultiplexing mixed oriented reads

#764 luigallucci opened 3 months ago
5
Error in file.py, "OutStream" object does not have attribute 'buffer'

#763 karenyun closed 4 months ago
3
Use `--action=lowercase` for short reads but keep trimmed passed reads.

#762 y9c closed 4 months ago
2
Remote File Support for input files

#761 geertvandeweyer opened 4 months ago
5
When demultiplexing, report contains irrelevant line

#760 marcelm opened 4 months ago
0
Add admonition about info-file w/r/t paired end mode

#759 odoublewen closed 4 months ago
1
NextSeq Quality Trimming Issue

#758 gfill88 closed 4 months ago
3
feature request: ubam support?

#757 eboyden opened 5 months ago
4
Make Cutadapt portable on macOS

#756 DmitriiSukhomlinov closed 5 months ago
11
ERROR: Error in sequence file at unknown line: Reads are improperly paired

#755 starz77 closed 5 months ago
2
sc/snATAC-seq barcode correction

#754 sknaack opened 5 months ago
5
poly-A trimming for paired-end data - consider orientation

#753 benemead opened 5 months ago
2
Installation instructions need conda channel

#752 susheelbhanu closed 5 months ago
2
Question about the paired-end read trimming.

#751 chaibenl opened 5 months ago
1
Fix issue with long adapters for kmer finder

#750 rhpvorderman closed 6 months ago
1
KmerFinder: x of length y is longer than the maximum of 64

#749 marcelm closed 6 months ago
1
Follow best practices for pointer aliasing in alignment inner loop.

#748 rhpvorderman closed 6 months ago
3
Feature request: ONT Chimeric read splitting

#747 rhpvorderman opened 6 months ago
1
paired fasta input with multiple cores

#746 bernt-matthias closed 6 months ago
7
Catching ONT adapters: allow setting insertion and deletion scores

#745 rhpvorderman closed 6 months ago
4
How to handle reads with alternative adapters or primer sequences

#744 fxfish closed 6 months ago
4
Small ONT optimization: length filtering before applying trimming

#743 rhpvorderman opened 7 months ago
1
Write a user guide specifically for ONT data

#742 rhpvorderman opened 7 months ago
18