Issues

• Support for path-cover output?

  COMBINE-lab/cuttlefish#70 · Filter by author RagnarGrootKoerkamp opened on Sep 28, 2026

• Is there any way to get the connectivity information when using cuttlefish 2?

  COMBINE-lab/cuttlefish#59 · Filter by author ctb opened on Oct 26, 2025

• Cuttlefish as a genome assembler?

  COMBINE-lab/cuttlefish#57 · Filter by author artorias111 opened on Apr 9, 2025

• Make install cuttlefish3

  COMBINE-lab/cuttlefish#56 · Filter by author karlisdaga opened on Mar 25, 2025

• CF3 outputs almost nothing when run on 2505 human genomes

  COMBINE-lab/cuttlefish#53 · Filter by author sebschmi opened on Mar 4, 2025

• Cuttlefish3 segfaults randomly on a standard E.coli pangenome

  COMBINE-lab/cuttlefish#52 · Filter by author sebschmi opened on Feb 24, 2025
  4

• Segfault when running on AllTheBacteria dataset

  COMBINE-lab/cuttlefish#48 · Filter by author sebschmi opened on Jan 13, 2025

• Cuttlefish 2 complains that the file kmc_01999_100_100.bin cannot be opened

  COMBINE-lab/cuttlefish#47 · Filter by author sebschmi opened on Jan 3, 2025
  3

• Obtaining unitig coordinates

  question
  COMBINE-lab/cuttlefish#46 · Filter by author revinici opened on Nov 20, 2024
  1

• KMC compilation error when compiling from source

  COMBINE-lab/cuttlefish#45 · Filter by author Sawwave opened on Oct 2, 2024
  8

• Using $TMPDIR as default temp working folder?

  enhancement
  COMBINE-lab/cuttlefish#41 · Filter by author tseemann opened on Jun 24, 2024
  2

• arm64 Cuttlefish on bioconda

  COMBINE-lab/cuttlefish#38 · Filter by author aryakaul opened on Dec 5, 2023
  4

  

• Reduced GFA output --> GFA1/GFA2 Output

  feature request
  COMBINE-lab/cuttlefish#37 · Filter by author aryakaul opened on Nov 2, 2023
  1

• Would you mind providing a more detail on assembly ?

  COMBINE-lab/cuttlefish#31 · Filter by author deyuanyang opened on Apr 22, 2023
  2

• Patch step error while linking library with CMake

  COMBINE-lab/cuttlefish#28 · Filter by author rlorigro opened on Mar 3, 2023
  3

• is there a way to get the kmer counts of the kmers in the produced unitigs?

  feature requestquestion
  COMBINE-lab/cuttlefish#27 · Filter by author shokrof opened on Feb 27, 2023
  4

• Extra large kmer

  enhancement
  COMBINE-lab/cuttlefish#22 · Filter by author apaytuvi opened on Oct 21, 2022
  6

• Potential arm support?

  enhancement
  COMBINE-lab/cuttlefish#19 · Filter by author michaelbarton opened on Oct 7, 2022
  3

  

• Cuttlefish as C++ API / header library?

  feature request
  COMBINE-lab/cuttlefish#7 · Filter by author Krannich479 opened on Feb 15, 2021
  2

  

• question on graph compaction

  question
  COMBINE-lab/cuttlefish#5 · Filter by author kevyin opened on Feb 5, 2021
  1