Source code related to Logan

All repositories cited in the Methods section of the Logan paper are listed below, grouped by whether the code was written for Logan or is existing third-party software used by Logan. All repositories have been archived on Zenodo for permanent access:

Zenodo archive: https://zenodo.org/records/20241498
DOI: https://doi.org/10.5281/zenodo.20241498

Logan-specific code

Code written for the Logan project, hosted across the contributing labs.

Core infrastructure

• Cloud infrastructure used to construct Logan : https://gitlab.pasteur.fr/rchikhi_pasteur/erc-unitigs-prod/ (solely intended for internal usage due to its high execution costs)
• f2sz, the block variant of Zstandard developed for FASTA-aligned random access : https://github.com/asl/f2sz
• Logan documentation and data access tutorial : https://github.com/IndexThePlanet/Logan

Search and indexing

• Logan-DIAMOND and Logan-minimap2 shallow/deep homology search pipeline : https://gitlab.pasteur.fr/rchikhi_pasteur/logan-analysis

Downstream analyses

• Logan50 protein clustering infrastructure : https://github.com/leejoey0921/cluster-logan/
• Plasmid identification via circular contig detection : https://gitlab.pasteur.fr/rchikhi_pasteur/logan-circles
• reorient-circular-seq, used in the plasmid pipeline to shift sequence breakpoints to intergenic regions : https://github.com/apcamargo/reorient-circular-seq
• PETadex plastic-active enzyme search : https://github.com/ababaian/petadex
• P4 phage satellite expansion : https://github.com/kdcurry/P4-logan
• AMR gene discovery : https://github.com/mmontonerin/logan_AMR
• FracMinHash sketching of Logan metagenomes : https://github.com/KoslickiLab/ingest_logan_yacht_data
• GenBank WGS vs Logan metagenome comparison : https://github.com/KoslickiLab/GenBank_WGS_analysis
• SRA geographical metadata extraction and enrichment : https://github.com/serratus-bio/logan-backend

Third-party tools used in Logan

Forks

• Cuttlefish2 fork with per-unitig abundance tracking, used for unitig assembly : https://github.com/rchikhi/cuttlefish (commit 9401ef5)
• kmtricks kmtricks-logan tag, used to build the Logan-Search index : https://github.com/tlemane/kmtricks

Used unmodified

• Minia3 contig assembler : https://github.com/GATB/minia (commit 71484e8)
• kmviz query result visualization, on which the Logan-Search front-end is based : https://github.com/tlemane/kmviz