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ab_genomed_qc

Assess Acinetobacter baumannii genomes quality on the nucleotide level

add_locustag_gbk_embl

Adds locus tag to GenBank and EMBL format files.

aln_stats_prot

Script producing protein alignment variants statistics

d3

Bring data to life with SVG, Canvas and HTML. :bar_chart::chart_with_upwards_trend::tada:

demux_i7

Demultiplex paired-end reads based only the i7 index

docker_patric_cli_1.039

Dockerized version of PATRIC CLI v.1.039

evo-ngs-refprep

Preparation of reference genome for variant calling pipeline

extract_aln_columns

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

get_taxonomy_by_ncbi_taxid

Get linage string by NCBI TaxID

github-slideshow

A robot powered training repository :robot:

ijump

Software to search rearrangements in population sequencing data

isfinder-sequences

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

metaphlan2_to_qiime

Convert Metaphlan2 format to QIIME format

morbido

R package for processing morbidostat v.1 log files

morbidostat_construction

Building Osterman Lab implementation of morbidostat

morbidostat_v2_construction

panmap

nucmer wrapper for mapping multiple close related genomes on a reference

paper_cipro_ec_ab_pa_2021

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

patric_gto_tools

Scripts to convert PATRIC gto format to other formats

subpop_decompose_gd

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

subpop_decompose_mip

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

triclosan_ee_paper

Experimental evolution of E. coli with exposure to triclosan

u50

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

wordly_helper

Shiny app aims to help choose words for WORDLY game