Issues

• polyG with low quality end remains even with --trim_poly_g option

  OpenGene/fastp#731 · Filter by author Yoonsung1203 opened on Oct 12, 2026

• [Feature Request] - Support for "auto" detect of adapters with properly paired interleaved reads from stdin

  OpenGene/fastp#730 · Filter by author jolespin opened on Oct 2, 2026

• Adapter trimming: one-gap search only compares the read start, so indel adapters are missed and reads that start like the adapter get trimmed

  OpenGene/fastp#728 · Filter by author dougnukem opened on Sep 29, 2026

• Feature request: Add merged reads statistics to report

  OpenGene/fastp#724 · Filter by author DeondeJager opened on Sep 25, 2026

• Feature request: optional paired-end read identifier validation

  OpenGene/fastp#720 · Filter by author thierrygosselin opened on Sep 6, 2026

• fastp misses reads when input fq.gz is made by concatenating multiple gzipped files (regression: fine in v1.1.0, broken in v1.3.6)

  OpenGene/fastp#711 · Filter by author yuanhetian1264 opened on Aug 20, 2026
  1

• poly-G trimming should occur before quality trimming

  OpenGene/fastp#710 · Filter by author eboyden opened on Aug 15, 2026

• Feature request: Auto-recognise sequencing instrument from FASTQ

  OpenGene/fastp#709 · Filter by author bounlu opened on Aug 7, 2026

• Error when installing from source (fatal error: hwy/foreach_target.h: No such file or directory)

  OpenGene/fastp#708 · Filter by author guidohooiveld opened on Jul 13, 2026
  2

• Infinite hang/deadlock when processing desynchronized PE reads ("different read numbers of the pack")

  OpenGene/fastp#694 · Filter by author vaishnavigawde-01 opened on May 12, 2026
  4

• Lowercase adapter auto-detected

  OpenGene/fastp#693 · Filter by author schorlton-bugseq opened on May 6, 2026
  1

• Feature request for base correction for PE data

  OpenGene/fastp#692 · Filter by author asilvestris84 opened on May 4, 2026

• Feature request: tile-level QC partitioning via regex on read name

  enhancement
  OpenGene/fastp#691 · Filter by author jdidion opened on May 4, 2026
  1

• Feature request: standalone adapter-detection subcommand

  enhancement
  OpenGene/fastp#690 · Filter by author jdidion opened on May 4, 2026
  1

• Feature request: library-type presets for common sequencing workflows

  OpenGene/fastp#689 · Filter by author jdidion opened on May 4, 2026

• Feature request: empirical sequencing-error-rate estimation

  enhancement
  OpenGene/fastp#688 · Filter by author jdidion opened on May 4, 2026
  1

• fastp v1.3.2: -w does not bound total CPU usage (regression from older versions)

  OpenGene/fastp#685 · Filter by author RAHenriksen opened on Apr 20, 2026
  1

• Automatic adapter detection detects ~1000x fewer adapter trimmed reads compared to specifying TruSeq adapters manually

  OpenGene/fastp#673 · Filter by author pmoris opened on Mar 23, 2026

• adding -overlap_len_require changes the PE adaptor trimming outcome

  OpenGene/fastp#664 · Filter by author reykeryao opened on Mar 9, 2026

• For batch processing of paired ends, fastp is unable to recognise samples as paired if -1 and -2 arguments are _1.fastq.gz and _2.fastq.gz instead of _1.fastq and _2.fastq

  OpenGene/fastp#661 · Filter by author jonng1000 opened on Feb 10, 2026
  1

• fail to trim polyT for some reads

  OpenGene/fastp#660 · Filter by author haibol2016 opened on Feb 6, 2026

• Add lack of support for auto-detection from stdin to the docs

  OpenGene/fastp#658 · Filter by author mikemc opened on Jan 29, 2026

• Fastp hangs when out of memory instead of throwing OOM

  OpenGene/fastp#657 · Filter by author James-S-Santangelo opened on Jan 26, 2026
  1

• output every failing criteria to failed_out

  OpenGene/fastp#653 · Filter by author tolot27 opened on Jan 20, 2026

• with illumina single why are there more reads after filtering?

  OpenGene/fastp#650 · Filter by author robertwhbaldwin opened on Jan 15, 2026