Topic: bacteria Goto Github
Some thing interesting about bacteria
Some thing interesting about bacteria
bacteria,Pan-genome wide association studies
User: admiralenola
bacteria,DecontaMiner is a tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data. It can suggest the presence of contaminating organisms in sequenced samples, that might derive either from laboratory contamination or from their biological source, and in both cases can be considered as worthy of further investigation and experimental validation. The novelty of DecontaMiner is mainly represented by its easy integration with the standard procedures of NGS data analysis, while providing a complete, reliable, and automatic pipeline. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2684-x
User: amarinderthind
Home Page: http://www-labgtp.na.icar.cnr.it/decontaminer/
bacteria,A convenient pipeline for processing of multi-strain bacterial RNA-Seq experiments
User: apredeus
bacteria,BSR-Based Allele Calling Algorithm
Organization: b-ummi
bacteria,PopPUNK 👨🎤 (POPulation Partitioning Using Nucleotide Kmers)
Organization: bacpop
Home Page: https://www.bacpop.org/poppunk
bacteria,Deep Learning-Based Object Detection and Bacteria Morphological Feature Extraction for Antimicrobial Resistance Applications
Organization: biodatlab
bacteria,🦠📇 Microbial genomes-to-report pipeline
User: cmkobel
Home Page: https://CompareM2.readthedocs.io
bacteria,BACTpipe: An assembly and annotation pipeline for bacterial genomics
Organization: ctmrbio
Home Page: https://bactpipe.readthedocs.org
bacteria,A spatially explicit trait- and individual-based microbial systems modelling framework
Organization: dement-model
bacteria,Software to predict the occurence of programmed ribosomal frameshifting in bacterial, phage, and viral genomes
User: deprekate
bacteria,GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
Organization: ecogenomics
Home Page: https://ecogenomics.github.io/GTDBTk/
bacteria,GET_HOMOLOGUES: a versatile software package for pan-genome analysis
User: eead-csic-compbio
bacteria,A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima
Organization: engqvistlab
bacteria,Bacterial Epigenomics Analysis SuiTe
Organization: fanglab
bacteria,Bacterial analysis toolbox for full ESKAPE pathogen characterization and profiling the resistome, mobilome, virulome & phylogenomics using WGS
User: gunzivan28
bacteria,viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data
Organization: icbi
bacteria,Artificial agents developing chemotaxis using probabilistic spiking perceptrons
User: jakobstenseke
bacteria,Phylogenetic compression of extremely large genome collections [661k ↘𝟭𝟲𝗚𝗶𝗕 | BIGSIdata ↘𝟰𝟴𝗚𝗶𝗕 | AllTheBact'23 ↘𝟳𝟱𝗚𝗶𝗕]
User: karel-brinda
Home Page: https://brinda.eu/mof
bacteria,Alignment against all pre-2019 bacteria on laptops within a few hours (former MOF-Search)
User: karel-brinda
Home Page: http://brinda.eu/mof
bacteria,Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
User: kjolley
Home Page: https://pubmlst.org/software/bigsdb/
bacteria,Build a partitioned pangenome graph from microbial genomes
Organization: labgem
Home Page: https://ppanggolin.readthedocs.io
bacteria,Bacterial taxonomy construction and evaluation in R
User: lmc297
bacteria,Genome scale metabolic models in SBML format
User: m-jahn
bacteria,Evaluating Nanopore-based bacterial variant calling
User: mbhall88
Home Page: https://doi.org/10.1101/2024.03.15.585313
bacteria,SEER, reimplemented in python 🐍🔮
User: mgalardini
Home Page: http://pyseer.readthedocs.io
bacteria,Simple counting of bacterial colonies from pictures of plates.
User: microbialman
bacteria,A pipeline to identify pathogenic microorganisms from scRNA-seq raw data.
User: ncrna
bacteria,A bioinformatic toolkit to align genome assemblies into pangenome graphs
Organization: neherlab
Home Page: https://neherlab.github.io/pangraph
bacteria,A comprehensive, compact, and automatically curated 16S database
Organization: ohnosequences
bacteria,A scalable bacterial genome assembly, annotation and analysis pipeline
User: oschwengers
Home Page: https://doi.org/10.1371/journal.pcbi.1007134
bacteria,Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
User: oschwengers
bacteria,Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.
User: oschwengers
Home Page: https://doi.org/10.1099/mgen.0.000398
bacteria,Targeted Detection and Reconstruction of Plasmids
User: oschwengers
bacteria,A simple pipeline for bacterial assembly and quality control
Organization: phac-nml
Home Page: https://phac-nml.github.io/mikrokondo/
bacteria,Hardware and software for accessible, extensible, and scalable bioreactors. Built on Raspberry Pi.
Organization: pioreactor
Home Page: https://pioreactor.com
bacteria,Accurate, resource-frugal and deterministic DNA sequence classifier.
Organization: prophyle
Home Page: https://prophyle.github.io
bacteria,Order and orientation of complete bacterial genomes
Organization: quadram-institute-bioscience
Home Page: https://doi.org/10.1099/mgen.0.000396
bacteria,Bacterial video tracking & analysis
User: schwanbeck
bacteria,Inofficial R client for the DSMZ's Bacterial Diversity Metadatabase (former contact: @katrinleinweber). https://api.bacdive.dsmz.de/client_examples seems to be the official alternatives.
Organization: tibhannover
Home Page: https://TIBHannover.GitHub.io/BacDiveR/
bacteria,:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
User: tseemann
bacteria,:scissors: :zap: Rapid haploid variant calling and core genome alignment
User: tseemann
bacteria,A curated list of phage related software and computational resources for phage scientists, bioinformaticians and enthusiasts.
User: voorloopnul
bacteria,A simulation of protozoan behavior and evolution
User: zebbeni
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