Issues

• potentially an issue with fetchNt.sh

  bbushnell/BBTools#35 · Filter by author genignored opened on Sep 15, 2026

• Issue with BBMerge resulting in 0 outcome

  bbushnell/BBTools#34 · Filter by author AndriiTarieiev opened on Sep 10, 2026
  1

• bug: bbmap ambig=random allows split alignments even with killbadpairs

  bbushnell/BBTools#33 · Filter by author eboyden opened on Aug 22, 2026

• feature request: bbmap recognize interleaved bam input

  bbushnell/BBTools#32 · Filter by author eboyden opened on Aug 16, 2026

• bug: bbmap aligned reads have chr "*" when outputting in BAM format

  bbushnell/BBTools#31 · Filter by author eboyden opened on Aug 6, 2026
  6

• feature request: optionally add MC and MQ tags to bbmap output

  bbushnell/BBTools#30 · Filter by author eboyden opened on Aug 5, 2026

• feature request: update bbmap to SAM spec 1.6 and add GO:query to the @HD line for paired read alignments

  bbushnell/BBTools#29 · Filter by author eboyden opened on Aug 5, 2026

• gradebins.sh error with gtdb

  bbushnell/BBTools#28 · Filter by author michoug opened on Jul 16, 2026
  1

• quickbin support for jgi_summarize_bam_contig_depths outputs

  bbushnell/BBTools#27 · Filter by author GeoMicroSoares opened on Jun 25, 2026

• bbduk fails with gzipped paired reads

  bbushnell/BBTools#26 · Filter by author SethMusker opened on Jun 17, 2026
  5

• github tagged archive and sourceforge tagged archives differs :: SF missing class files

  bbushnell/BBTools#25 · Filter by author EricDeveaud opened on Jun 17, 2026

• sendsketch/TaxServer returns HTTP 400 (NumberFormatException) for single-k sketch servers (e.g. k=31)

  bbushnell/BBTools#23 · Filter by author rec3141 opened on Jun 11, 2026
  1

• sequences > 500 mb

  bbushnell/BBTools#21 · Filter by author gribskov opened on May 26, 2026
  3

• quickbin.sh yields 0 coverage for all contigs when inputting bwa mem SAM files

  bbushnell/BBTools#20 · Filter by author ucassee opened on May 25, 2026
  3

• AssertionError: negative extraPadLeft/Right in TranslateColorspaceRead.realign_new on spliced long reads (greflen overflow)

  bbushnell/BBTools#19 · Filter by author k-roy opened on May 19, 2026
  1

• calctruequality.sh - Exception in thread "main" java.lang.AssertionError with callvars

  bbushnell/BBTools#18 · Filter by author masalgar opened on Apr 14, 2026
  1

• Aggressive Sequence Identifier Truncation with ignorejunk=t in filterbyname.sh v39.62

  bbushnell/BBTools#17 · Filter by author mmokrejs opened on Apr 3, 2026
  4

• Specify memory requirements with environment variables

  bbushnell/BBTools#16 · Filter by author prototaxites opened on Apr 1, 2026

• changelog updates

  bbushnell/BBTools#15 · Filter by author OH-AU opened on Mar 31, 2026

• Support java option -Djava.io.tmpdir

  bbushnell/BBTools#13 · Filter by author fgvieira opened on Mar 25, 2026

• Shuffle2 AssertionError

  bbushnell/BBTools#12 · Filter by author JavierMenRev opened on Mar 13, 2026

• BBNorm - List size mismatch Assertion Error when Forward and Reverse Reads are not the same length

  bbushnell/BBTools#11 · Filter by author zacherydickson opened on Mar 9, 2026
  1

• bug: bbmerge.sh hangs on v39.56 and up

  bbushnell/BBTools#10 · Filter by author eboyden opened on Mar 7, 2026
  3

• Error in FASTQ, record 0, with these 4 lines: (missing plus)

  bbushnell/BBTools#9 · Filter by author schorlton-bugseq opened on Feb 24, 2026

• [BUG?] Unable to recognize fq.gz file as a gzip file

  bbushnell/BBTools#8 · Filter by author hellopeccat opened on Jan 9, 2026
  1