Logan: source code archive

Archive of the source code repositories referenced in the Methods section of the Logan paper (Chikhi et al., 2026, bioRxiv: https://www.biorxiv.org/content/10.1101/2024.07.30.605881v2). For each repository, two files are provided:

• <name>.tar.gz — source tree at the commit used in the paper, with the .git directory stripped.
• <name>.bundle — full git history as a git bundle. Restore with git clone <name>.bundle.

Repositories archived:

• IndexThePlanet-Logan.tar.gz / IndexThePlanet-Logan.bundle — https://github.com/IndexThePlanet/Logan @ 71f065623a
  Main Logan documentation, data access tutorial, and Code.md index
• rchikhi-cuttlefish.tar.gz / rchikhi-cuttlefish.bundle — https://github.com/rchikhi/cuttlefish @ 9401ef54c0
  Modified Cuttlefish2 used for unitig assembly (commit pinned in paper)
• GATB-minia.tar.gz / GATB-minia.bundle — https://github.com/GATB/minia @ 71484e8e7d
  Minia3 contig assembler (commit pinned in paper)
• asl-f2sz.tar.gz / asl-f2sz.bundle — https://github.com/asl/f2sz @ f03329c86f
  Block variant of Zstandard for FASTA-aligned compression
• erc-unitigs-prod.tar.gz / erc-unitigs-prod.bundle — https://gitlab.pasteur.fr/rchikhi_pasteur/erc-unitigs-prod @ 43c4215ab7
  Cloud infrastructure used to construct Logan
• tlemane-kmtricks.tar.gz / tlemane-kmtricks.bundle — https://github.com/tlemane/kmtricks @ 7f27438195
  kmtricks used to index all k-mers (tag pinned in paper)
• tlemane-kmviz.tar.gz / tlemane-kmviz.bundle — https://github.com/tlemane/kmviz @ 43be0e5b89
  Visualization interface for Logan-Search
• logan-analysis.tar.gz / logan-analysis.bundle — https://gitlab.pasteur.fr/rchikhi_pasteur/logan-analysis @ 5e92dafb87
  Pipeline for Logan-DIAMOND and Logan-minimap2 homology search
• leejoey0921-cluster-logan.tar.gz / leejoey0921-cluster-logan.bundle — https://github.com/leejoey0921/cluster-logan @ feb05a64f8
  Infrastructure for clustering Logan50 proteins
• ababaian-petadex.tar.gz / ababaian-petadex.bundle — https://github.com/ababaian/petadex @ a6bc326eb1
  PETadex plastic-active enzyme data and code
• kdcurry-P4-logan.tar.gz / kdcurry-P4-logan.bundle — https://github.com/kdcurry/P4-logan @ 36c4319368
  P4 phage satellite analysis scripts
• logan-circles.tar.gz / logan-circles.bundle — https://gitlab.pasteur.fr/rchikhi_pasteur/logan-circles @ f8d2a75b68
  Plasmid identification via circular contig detection
• apcamargo-reorient-circular-seq.tar.gz / apcamargo-reorient-circular-seq.bundle — https://github.com/apcamargo/reorient-circular-seq @ 360a63af98
  Reorient circular sequences to shift breakpoints to intergenic regions
• mmontonerin-logan_AMR.tar.gz / mmontonerin-logan_AMR.bundle — https://github.com/mmontonerin/logan_AMR @ ce78e14d5e
  AMR gene discovery analyses
• KoslickiLab-ingest_logan_yacht_data.tar.gz / KoslickiLab-ingest_logan_yacht_data.bundle — https://github.com/KoslickiLab/ingest_logan_yacht_data @ 6830a02565
  FracMinHash sketch ingestion of Logan metagenomes
• KoslickiLab-GenBank_WGS_analysis.tar.gz / KoslickiLab-GenBank_WGS_analysis.bundle — https://github.com/KoslickiLab/GenBank_WGS_analysis @ a2b5e5dce8
  GenBank WGS vs Logan metagenome sketch comparison
• serratus-bio-logan-backend.tar.gz / serratus-bio-logan-backend.bundle — https://github.com/serratus-bio/logan-backend @ b5dc42d15c
  Curated SRA geographical metadata

The MANIFEST.txt file maps each archive name to its upstream URL, the requested reference (commit or tag), and the resolved commit hash.