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  • skDER Public

    skDER & CiDDER: efficient & high-resolution dereplication of microbial genomes to select representatives for comparative genomics and metagenomics.

    Python 41 3 BSD 3-Clause "New" or "Revised" License Updated Dec 20, 2024
  • zol Public

    Forked from Kalan-Lab/zol
    Python BSD 3-Clause "New" or "Revised" License Updated Dec 3, 2024
  • Conda recipes for the bioconda channel.

    Shell MIT License Updated Nov 19, 2024
  • raufs Public

    BSD 3-Clause "New" or "Revised" License Updated Sep 12, 2024
  • codoff Public

    Forked from Kalan-Lab/codoff

    codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, phage, etc.) relative to the full genome.

    Python BSD 3-Clause "New" or "Revised" License Updated Jul 31, 2024
  • Directory with GTDB GCA accession to taxonomy mappings used by various programs.

    Creative Commons Attribution 4.0 International Updated May 9, 2024
  • lsaBGC Public

    Forked from Kalan-Lab/lsaBGC

    lsaBGC - Lineage Specific Analysis of Biosynthetic Gene Clusters

    Python BSD 3-Clause "New" or "Revised" License Updated May 1, 2024
  • Suite to delineate contiguous and conserved sequences from assemblies and search for their presence in raw sequencing data.

    Python BSD 3-Clause "New" or "Revised" License Updated Jul 13, 2023
  • Phylogenetic orthology inference for comparative genomics

    Python GNU General Public License v3.0 Updated Jun 1, 2023
  • BiG-MAP Public

    Forked from medema-group/BiG-MAP
    Python 1 Other Updated Jul 17, 2022
  • HTML Updated Jan 2, 2021
  • Jupyter Notebook MIT License Updated Jan 2, 2021
  • minima Public

    Forked from jekyll/minima

    Minima is a one-size-fits-all Jekyll theme for writers.

    SCSS MIT License Updated Dec 29, 2020
  • seQuoia Public

    Forked from broadinstitute/seQuoia

    A framework for diverse omics workflows, primarily focused on QC, processing and analysis of bacterial genomic sequencing sets.

    Python GNU General Public License v3.0 Updated Dec 22, 2020
  • Programs developed for rotation in the Anantharaman lab, includes MetaDownSampler.py - which takes in a metagenome assembly and a BAM file containing self/reflexive alignment of reads to the assemb…

    Python MIT License Updated Sep 30, 2020
  • Code and programs developed for Tn-Seq analysis of E. faecalis MMH594.

    Python BSD 3-Clause "New" or "Revised" License Updated Sep 14, 2020
  • Creation of a database of Genbank genomes including isolate reference genomes and MAGs, and parallelizing 1000s of genome searches for a specific marker

    Python Updated Apr 28, 2020
  • Admixture Public

    Forked from jacahill/Admixture
    C++ GNU General Public License v3.0 Updated Feb 13, 2020