indexofire

indexofire's Stars

• cmdcolin/awesome-genome-visualization

  A list of interesting genome browser and genome visualization programs

  Language:TypeScript8792810112

• pachterlab/kallisto

  Near-optimal RNA-Seq quantification

  Language:C66548378173

• Ecogenomics/GTDBTk

  GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

  Language:Python4882346682

• nanoporetech/medaka

  Sequence correction provided by ONT Research

  Language:Python4304851476

• HKU-BAL/Clair3

  Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

  Language:Python2501130730

• BioOmics/iSeq

  Download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.

  Language:Shell13611910

• EBI-Metagenomics/emg-viral-pipeline

  VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies

  Language:Python12877216

• esteinig/nanoq

  Minimal but speedy quality control for nanopore reads in Rust :bear:

  Language:Rust12754210

• nmquijada/tormes

  Making whole bacterial genome sequencing data analysis easy

  Language:Shell10157132

• robotoD/GenoVi

  GenoVi, an automated customizable circular genome visualizer for bacteria and archaea

  Language:Python8742111

• AllTheBacteria/AllTheBacteria

  Follow up to Grace Blackwell's 661k dataset, for 2023

  Language:Python8624465

• rrwick/Metagenomics-Index-Correction

  Language:Python792139

• kjolley/BIGSdb

  Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.

  Language:Perl65999720

• aakechin/NGS-PrimerPlex

  NGS-PrimerPlex is a high-throughput tool for mupltiplex primer design

  Language:Python5556122

• phac-nml/ecoli_serotyping

  In silico prediction of E. coli serotype

  Language:Python5082011

• theiagen/public_health_bioinformatics

  Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.

  Language:WDL38833818

• Carrion-lab/bacLIFE

  Language:Python353195

• pbloem/pca-book

  Source files for a book on Principal component analysis

  Language:TeX34120

• typhoidgenomics/genotyphi

  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)

  Language:Python2451010

• CDCgov/aquascope

  Language:Nextflow1792710

• symgenoevolab/SyntenyFinder

  SyntenyFinder contains a collection of scripts to easily perform and visualize macrosynteny analysis when provided with the accessions of annotated chromosome-level genome assemblies from NCBI.

  Language:Jupyter Notebook17247

• CFSAN-Biostatistics/bettercallsal

  Nextflow workflows to assign Salmonella serotype based on Genome similarity using MASH, SOURMASH and KMA.

  Language:Nextflow11821

• genomic-medicine-sweden/gms-artic

  A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).

  Language:Nextflow103296

• CHRF-Genomics/Paratype

  Assign genotypes to Salmonella Paratyphi A isolates using their whole-genome data.

  Language:Python8131

• davideyre/hash-cgmlst

  Language:R8044

• shengzheBian/VPsero

  rapid serotyping of Vibrio parahaemolyticus from whole genome sequencing data using serogroup-specific genes

  Language:Python8210

• SionBayliss/HierarchicalML

  Hierarchical ML Package with example application for Salmonella Enteritidis

  Language:HTML8412

• typhoidgenomics/TyphiNET

  TyphiNET online Salmonella Typhi AMR surveillance dashboard.

  Language:JavaScript84293

• infinity-a11y/PhyloTrace

  PhyloTrace is a GUI platform for bacterial monitoring offering a toolkit of analyses like hashed cgMLST typing and Antimicrobial Resistance Screening.

  Language:R5210

• pathogenwatch-oss/vista

  The Pathogenwatch Vibrio cholerae genotyping tool

  Language:Python5100