yujiehu0823

yujiehu0823's Stars

• phac-nml/ecoli_serotyping

  In silico prediction of E. coli serotype

  Language:Python5111

• SBRG/precise-db

  A high-fidelity E. coli RNA-seq compendium

  Language:Jupyter Notebook3219

• vmingchen/PacBioAssembly

  Assemble E. coli's genome from long reads with high error rate from PacBio

  Language:C++52

• behrimg/MuriSam

  Scripts to assemble and analyze genomes for E. coli populations and clones

  Language:Shell32

• superphy/kmer

  Using machine learning to predict E. coli phenotypes

  Language:TeX12

• DerrickWood/kraken2

  The second version of the Kraken taxonomic sequence classification system

  Language:C++749273

• phac-nml/sistr_cmd

  SISTR (Salmonella In Silico Typing Resource) command-line tool

  Language:Python269

• katholt/typhoid

  1

• klebgenomics/Kleborate

  Language:Python11849

• kblin/ncbi-genome-download

  Scripts to download genomes from the NCBI FTP servers

  Language:Python971173

• ParBLiSS/FastANI

  Fast Whole-Genome Similarity (ANI) Estimation

  Language:C++38567

• lskatz/mashtree

  :deciduous_tree: Create a tree using Mash distances

  Language:Perl15725

• marbl/parsnp

  Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.

  Language:C++13225

• arpcard/rgi

  Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

  Language:Python34378

• arpcard/amr_curation

  A public repository for collective curation of antimicrobial resistance (AMR) genes and mutations. Submit, discuss, and resolve AMR curation issues.

  586

• lipingfangs/Bacteriatool

  bacteriatool is a corpus of python script to deal with a lot of problem about bacteria genome analysis. you can use it to manage the data created by resfinder.py(https://bitbucket.org/genomicepidemiology/resfinder.git) to build a csv matrix about the presence of drug resistance genes in different individuals by Resfinder2csv.py. you can use it to manage the data created by toxicity database :VFDB by blast2.7(default output) to build a csv matrix about the presence of drug toxicity genes in different individuals by VFDB2csv.py. you can use it to extract the information like "organism","isolation_source","host","country","lat_lon","collection_date","sample_name" of GBK(GCA) file form NCBI and create a csv matrix of your information.

  Language:Python6

• phac-nml/staramr

  Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

  Language:Python12728

• typhoidgenomics/genotyphi

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

  Language:Python2410

• jhawkey/IS_mapper

  IS mapping software

  Language:Python5316

• katholt/NGSchallenge

  Data for the outbreak investigation software challenge session at the ASM NGS 2015 conference

  71

• katholt/plotTree

  Language:R6735

• ylxdzsw/mo-generator

  有针对性地表达自己的崇敬之心

  Language:JavaScript371

• katholt/srst2

  Short Read Sequence Typing for Bacterial Pathogens

  Language:Python12666

• OpenGene/MutScan

  Detect and visualize target mutations by scanning FastQ files directly

  Language:C14938

• OpenGene/fastp

  An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

  Language:C++2k334

• rrwick/Bandage

  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

  Language:C++59699

• rrwick/Unicycler

  hybrid assembly pipeline for bacterial genomes

  Language:C++578136

• tseemann/prokka

  :zap: :aquarius: Rapid prokaryotic genome annotation

  Language:Perl858228

• tseemann/snippy

  :scissors: :zap: Rapid haploid variant calling and core genome alignment

  Language:Perl492117

• tseemann/abricate

  :mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

  Language:Perl38394