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Achievement: YOLOAchievement: Pull SharkAchievement: Arctic Code Vault Contributor

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Achievement: YOLOAchievement: Pull SharkAchievement: Arctic Code Vault Contributor

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  • ijump Public

    Software to search rearrangements in population sequencing data

    Python 2 2 GNU General Public License v3.0 Updated Jun 1, 2024

  • ab_genomed_qc Public

    Assess Acinetobacter baumannii genomes quality on the nucleotide level

    Nextflow MIT License Updated Sep 16, 2022

  • aln_stats_prot Public

    Script producing protein alignment variants statistics

    Python 1 Updated Sep 8, 2022

  • github-slideshow Public

    A robot powered training repository 🤖

    HTML MIT License Updated Jul 7, 2022

  • evo-ngs-refprep Public

    Preparation of reference genome for variant calling pipeline

    Python 1 MIT License Updated Jun 14, 2022

  • patric_gto_tools Public

    Scripts to convert PATRIC gto format to other formats

    Perl 1 1 GNU General Public License v3.0 Updated Jun 14, 2022

  • docker_patric_cli_1.039 Public

    Dockerized version of PATRIC CLI v.1.039

    Dockerfile Updated Jun 7, 2022

  • subpop_decompose_mip Public

    Decompose observed variants to subpopulations using mixed integer programming with pulp package,

    Python 1 Updated Apr 5, 2022

  • add_locustag_gbk_embl Public

    Adds locus tag to GenBank and EMBL format files.

    Python GNU General Public License v3.0 Updated Mar 24, 2022

  • morbidostat_construction Public

    Building Osterman Lab implementation of morbidostat

    C++ 2 1 GNU General Public License v3.0 Updated Mar 7, 2022

  • wordly_helper Public

    Shiny app aims to help choose words for WORDLY game

    R GNU General Public License v3.0 Updated Feb 22, 2022

  • extract_aln_columns Public

    Extracts columns from alignment according to positions in the reference sequence.

    Python GNU General Public License v3.0 Updated Feb 7, 2022

  • subpop_decompose_gd Public

    Decomposition of population deep-sequencing data into subpopulations using gradient descend algorithm.

    Python 1 Updated Jan 24, 2022

  • morbidostat_v2_construction Public

    C++ 1 1 Updated Jan 17, 2022

  • ISfinder-sequences Public

    Forked from thanhleviet/ISfinder-sequences

    Insertion sequences (Insertion Element) [https://en.wikipedia.org/wiki/Insertion_sequence] collected from ISfinder (https://isfinder.biotoul.fr/)

    Updated Oct 7, 2021

  • d3 Public

    Forked from d3/d3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

    JavaScript ISC License Updated Jun 11, 2021

  • paper_cipro_EC_AB_PA_2021 Public

    Supplementary code for "Morbidostat-Directed Experimental Evolution of Ciprofloxacin Resistance in Gram-negative Bacterial Pathogens" paper.

    Python GNU General Public License v3.0 Updated Mar 18, 2021

  • Triclosan_EE_paper Public

    Experimental evolution of E. coli with exposure to triclosan

    Python 1 GNU General Public License v3.0 Updated Mar 10, 2021

  • MoRbido Public

    R package for processing morbidostat v.1 log files

    R Updated Dec 1, 2020

  • get_taxonomy_by_NCBI_TaxID Public

    Get linage string by NCBI TaxID

    Python 1 GNU General Public License v3.0 Updated Sep 30, 2020

  • demux_i7 Public

    Demultiplex paired-end reads based only the i7 index

    Python Updated Jun 16, 2020

  • U50 Public

    Forked from CDCgov/U50

    U50 : measuring assembly output based on non-overlapping, target-specific contigs

    Python Apache License 2.0 Updated Dec 6, 2019

  • metaphlan2_to_qiime Public

    Convert Metaphlan2 format to QIIME format

    Python 1 1 GNU General Public License v3.0 Updated Sep 26, 2019

  • panmap Public

    nucmer wrapper for mapping multiple close related genomes on a reference

    Python GNU General Public License v3.0 Updated Aug 13, 2019