jdalsdurf

jdalsdurf's Stars

• lh3/jstreeview

  Interactive phylogenetic tree viewer/editor

  Language:JavaScript463

• pkmitchell/VPECdb

  Veterinary Pathogenic E. coli database

  21

• phac-nml/refseq_masher

  Mash MinHash search your nucleotide sequences against a NCBI RefSeq genomes database

  Language:Jupyter Notebook393

• phac-nml/sistr_cmd

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

  Language:Python239

• UrbsLab/STREAMLINE

  Simple Transparent End-To-End Automated Machine Learning Pipeline for Supervised Learning in Tabular Binary Classification Data

  Language:Jupyter Notebook639

• phac-nml/ecoli_serotyping

  In silico prediction of E. coli serotype

  Language:Python4610

• PacktWorkshops/The-Python-Workshop

  A New, Interactive Approach to Learning Python

  Language:Jupyter Notebook249353

• fritzsedlazeck/Sniffles

  Structural variation caller using third generation sequencing

  Language:Python52586

• philres/ngmlr

  NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

  Language:C++28441

• rrwick/Trycycler

  A tool for generating consensus long-read assemblies for bacterial genomes

  Language:Python29828

• CDCgov/SARS-CoV-2_Sequencing

  A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.

  Language:Perl34483

• jenniferlu717/KrakenTools

  KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

  Language:Python29785

• bactopia/bactopia

  A flexible pipeline for complete analysis of bacterial genomes

  Language:Nextflow37465

• sanger-pathogens/snp-sites

  Finds SNP sites from a multi-FASTA alignment file

  Language:C23050

• edgardomortiz/vcf2phylip

  Convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis

  Language:Python27084

• zhaoc1/pangenome-snakemake

  Rules to run Roary or PanPhlAn to build pangenome using Snakemake

  Language:HTML61

• ngs-docs/2020-ggg-201b-variant-calling

  Language:Python41

• vpc-ccg/haslr

  A fast tool for hybrid genome assembly of long and short reads

  Language:C++749

• quinlan-lab/applied-computational-genomics

  Applied Computational Genomics Course at UU: Spring 2020

  Language:HTML922202

• jdalsdurf/spades

  SPAdes Genome Assembler

  1

• jdalsdurf/mlst

  :id: Scan contig files against PubMLST typing schemes

  1

• jdalsdurf/abricate

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

  1

• jdalsdurf/prokka

  :zap: :aquarius: Rapid prokaryotic genome annotation

  1

• jdalsdurf/minimap2

  A versatile pairwise aligner for genomic and spliced nucleotide sequences

  1

• jdalsdurf/RaGOO

  Fast Reference-Guided Scaffolding of Genome Assembly Contigs

  1

• jdalsdurf/Roary

  Rapid large-scale prokaryote pan genome analysis

  1

• tseemann/nullarbor

  :floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

  Language:Perl13137

• leipzig/SandwichesWithSnakemake

  This is a beginner's tutorial to Snakemake

  7012

• dohlee/snakemake-hamburger

  :snake::hamburger: A beginner's guide to modular snakemake workflows.

  Language:Python61

• malonge/RaGOO

  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag

  Language:Python16828