OpenGene/fastp issues and pull requests

#583 - Adapter Detection Issue with Paired-End Data in fastp Leading to Incomplete Trimming

Issue - State: open - Opened by Liping-L 22 days ago

#582 - merging read pair mates using a reference sequence

Issue - State: open - Opened by mmokrejs 23 days ago

#581 - merge paired-end reads: include average or even better median overlap length

Issue - State: open - Opened by mmokrejs 23 days ago

#579 - Disable "too many N" filter

Issue - State: open - Opened by matthdsm about 2 months ago

#578 - Different minimum lengths for the forward and reverse reads during filtering

Issue - State: closed - Opened by MariamFahmy about 2 months ago

#577 - Adapter sequences not removed from short SE data

Issue - State: open - Opened by MafGal about 2 months ago

#576 - Fastp does not remove G homopolymers

Issue - State: open - Opened by Homap about 2 months ago

#575 - Output read lengths are affected by duplicate --adapter_sequence arguments

Issue - State: open - Opened by mwhamgenomics 2 months ago

#574 - What are the default settings?

Issue - State: open - Opened by jiangzy26 2 months ago

#573 - Ability to use FASTA files as input

Issue - State: open - Opened by vkkodali 4 months ago

#572 - trimming adapters at the beginning of the read and IUPAC nucleotide codes

Issue - State: open - Opened by hrehrauer 4 months ago

#571 - Use with fifo?

Issue - State: open - Opened by GregTD42 4 months ago - 3 comments

#570 - How can I reproduce the results of trimmomatic in fastp?

Issue - State: open - Opened by jeong2624 4 months ago - 2 comments

#569 - Feature request: output file listing the IDs of duplicate reads and associated "representative reads"

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

#568 - How can I generate images of the same size as the insert fragment individually

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

#567 - typo in "forogt" -> "forgot"

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

#566 - Feature request: remove reads with poly_X tails and polyX in general

Issue - State: open - Opened by roni-fultheim 6 months ago

#565 - ERROR: '+' expected

Issue - State: open - Opened by spw6422 6 months ago - 5 comments

#564 - Feature Request: fastp operation on input and output directories

Issue - State: open - Opened by SuhasSrinivasan 6 months ago

#563 - Running fastp in quiet mode.

Issue - State: open - Opened by otradnaya 6 months ago - 2 comments

#562 - Not reproducible

Issue - State: open - Opened by jnmaloof 6 months ago - 7 comments

#561 - not support arm?

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

#560 - Error is raised for problematic rows

Issue - State: open - Opened by TomerAntman 6 months ago - 3 comments

#559 - few options throw 'undefined error' -reg

Issue - State: open - Opened by parima678 7 months ago

#558 - fastp not removing all Illumina universal adapter sequences as indicated by FastQC

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

#557 - No adapter detected for read and Q20 bases: 4747174600(99.9999%)

Issue - State: open - Opened by h20gg702 8 months ago

#556 - Highlight the new publication

Pull Request - State: closed - Opened by YongxinLiu 8 months ago

#555 - Nanopore data filtering using fastp

Issue - State: open - Opened by emilydolivo97 8 months ago - 1 comment

#554 - Keep occurred error message from the beginning < igzip: invalid gzip header found >

Issue - State: open - Opened by teddy-han 8 months ago

#553 - Not able to install on Mac book M1

Issue - State: open - Opened by ranijames 8 months ago - 4 comments

#552 - interleaved output is not reproducible with multiple threads

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

#551 - Split interleaved output

Issue - State: open - Opened by Poshi 8 months ago

#550 - Added a new function(umi_skipb) to the program to skip the specified bp number before trim the UMI sequence.

Pull Request - State: open - Opened by biolxy 9 months ago

#549 - Store duplicate reads

Issue - State: open - Opened by johnw2358 9 months ago

#548 - Interpretation help file?

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

#547 - Missing most reads after given r2 adapter

Issue - State: open - Opened by Flying-Doggy 9 months ago - 1 comment

#546 - minor typo fix

Pull Request - State: open - Opened by Gaura 9 months ago - 1 comment

#545 - cuting doesn't interfere with deduplication

Pull Request - State: open - Opened by SilasK 10 months ago

#544 - Fix typo

Pull Request - State: open - Opened by fplaza 10 months ago - 1 comment

#543 - Feature request: add option to set lower limit of unqualified quality

Issue - State: open - Opened by ybendana 10 months ago

#542 - Can fastq remove read sequences with duplicate IDs?

Issue - State: open - Opened by huangrongbioinfomation 10 months ago

#541 - No mouse ouver in kmer matrix

Issue - State: open - Opened by SilasK 10 months ago

#540 - Very short fragments

Issue - State: open - Opened by SilasK 10 months ago

#539 - Can fastp draw PNG format?

Issue - State: open - Opened by huangrongbioinfomation 10 months ago

#538 - aborted core dumped

Issue - State: open - Opened by ramnageena11 10 months ago

#537 - fastp in my pip package

Issue - State: open - Opened by theAguy 10 months ago

#536 - Insert size estimation and report interpretation

Issue - State: open - Opened by lmartinezgili 12 months ago - 2 comments

#535 - I obtained different 'insert size peaks' when I used different options for the same paired-end sequencing sample.

Issue - State: open - Opened by Eunyoung-Oh114 12 months ago

#534 - ERROR: '+' expected

Issue - State: open - Opened by wangsanshui1028 12 months ago - 1 comment

#533 - check read errors in fastqreader

Pull Request - State: open - Opened by jchorl about 1 year ago

#532 - Does fastp remove primer sequences for aplicon sequencing results?

Issue - State: open - Opened by timz0605 about 1 year ago - 1 comment

#531 - Adapter indels

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

#530 - Is `Read1 before filtering` field in the report filtered at all or is it the raw read count per mate?

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

#529 - Feature Request: UMI Join

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

#528 - Discrepency in filtering restults and reads after filtering

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

#527 - Add a Docker container

Pull Request - State: open - Opened by maol-corteva about 1 year ago

#526 - Hi guys, this feature is revised and improved a lot in fastp v0.19.9 (will be released soon), see the update here:

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

#525 - Remove the hardcoded trim tail and trim front length limitations

Pull Request - State: open - Opened by shinthor about 1 year ago

#524 - invalid gzip output when output is empty

Issue - State: open - Opened by sstrong99 about 1 year ago

#523 - Building a fastp binary on Apple Silicon

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

#522 - ./fastp: error while loading shared libraries: libisal.so.2: cannot open shared object file: No such file or directory

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

#521 - Error trimming reads - invalid gzip error found and sequence and quality have different lengths

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

#520 - Duplication

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

#519 - prebuilt fastp binary links for Linux are broken

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

#518 - fastp can not remove adapter when the read sequence has indels in the adpter

Issue - State: open - Opened by YangLeng90 over 1 year ago

#517 - Unable to read from named pipes

Issue - State: open - Opened by wasade over 1 year ago - 1 comment

#516 - FastQ contains reads header name only - ERROR: sequence and quality have different length

Issue - State: open - Opened by phucty over 1 year ago - 2 comments

#515 - Fix ReadPair's never being freed

Pull Request - State: open - Opened by Donwulff over 1 year ago

#514 - Is the statistics of "adapter_trimmed_reads" in the file correct?

Issue - State: open - Opened by wangjingint over 1 year ago

#513 - Merged reads restricted to length of the read pairs?

Issue - State: open - Opened by robinfchan over 1 year ago - 2 comments

#512 - UMI dedup

Issue - State: open - Opened by zoeward-nz over 1 year ago - 1 comment

#511 - PolyG tail trimming on already trimmed fastq files

Issue - State: open - Opened by DenisGoryunov over 1 year ago

#510 - question about pacbio data

Issue - State: open - Opened by crazysummerW over 1 year ago

#509 - fastp -i -I has multiple data -o -O how to write

Issue - State: open - Opened by hai178912522 over 1 year ago

#508 - Update list of sequencers for poly-g trimming

Pull Request - State: open - Opened by semenko over 1 year ago

#507 - can fastp be used to demultiplex fastq files based on indexes in the sequence header?

Issue - State: open - Opened by rikrdo89 over 1 year ago

#506 - Unstable and irreproducible results

Issue - State: open - Opened by roni-fultheim over 1 year ago - 2 comments

#505 - How to remove contaminated sequencing data

Issue - State: open - Opened by jiangzy26 over 1 year ago

#504 - issue trying to use fifo for inputs

Issue - State: open - Opened by splaisan over 1 year ago - 1 comment

#503 - No adapter detected for read2 and Insert size peak (evaluated by paired-end reads): 103

Issue - State: open - Opened by sofiapuvogelvittini over 1 year ago - 1 comment

#502 - Different adaptors detected in paired reads

Issue - State: open - Opened by sofiapuvogelvittini over 1 year ago - 2 comments

#501 - Can fastp trim TSO (Template switch oligo)?

Issue - State: open - Opened by yunshanglzy over 1 year ago

#500 - Cannot install fastp on my computer - channels not found

Issue - State: closed - Opened by vaizen360 over 1 year ago

#499 - output on command line of fastp is incorrect

Issue - State: open - Opened by atiqaahmad over 1 year ago

#498 - Length Limit stops working past a certain point

Issue - State: open - Opened by kaeaton over 1 year ago

#497 - Fix for 2 bugs in the fastq reader:

Pull Request - State: open - Opened by wdu over 1 year ago

#496 - How important is isa-l?

Issue - State: open - Opened by outpaddling over 1 year ago

#495 - fix average q-score calculation

Pull Request - State: open - Opened by DrinnanSante over 1 year ago

#494 - UMI extraction 3' end

Issue - State: open - Opened by annajbott over 1 year ago - 1 comment

#493 - cut_right doesn't work as the same as trimmomatic

Issue - State: open - Opened by Oakento over 1 year ago

#492 - is adapter file is unreadable return core dumped error

Issue - State: open - Opened by mewu3 over 1 year ago

#491 - ERROR: Read name line should start with '@'

Issue - State: closed - Opened by qquuzhao over 1 year ago - 12 comments

#490 - Update fastp pre-build version to v0.23.3

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

#489 - NextSeq auto-detect seems incomplete

Issue - State: open - Opened by claczny over 1 year ago

#488 - ¿Is it possible to install fastp in windows?

Issue - State: open - Opened by CamiloOcho over 1 year ago

#487 - Trim Read 1 and Read 2 independently without detecting overlap

Issue - State: open - Opened by MaWeffm over 1 year ago

#486 - Request: Tag a New Release

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

#485 - Change error message for interleaved stdout

Pull Request - State: closed - Opened by ElDeveloper over 1 year ago - 3 comments

#484 - Typo correction in options.cpp

Pull Request - State: closed - Opened by B0r1sD over 1 year ago

#483 - [mem_sam_pe] paired reads have different names:

Issue - State: open - Opened by YeGuoZJU over 1 year ago

GitHub / OpenGene/fastp issues and pull requests