hngyou's Stars
linsalrob/PhiSpy
Prediction of prophages from bacterial genomes
ptynecki/PHAGES2050
PHAGES2050 - a Comprehensive AI-based Framework for Phage Research & Therapy
cov-lineages/pangolin
Software package for assigning SARS-CoV-2 genome sequences to global lineages.
kjolley/BIGSdb
Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
GuangchuangYu/nCov2019
query stats of infected coronavirus cases
CDCgov/SARS-CoV-2_Sequencing
A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
artic-network/primer-schemes
Primer schemes for real-time genome epidemiology
kristyhoran/coreuscan
A tool for downloading Core Genome MLST schemes for bacterial genomics for use with chewBBACA
artic-network/artic-ncov2019
ARTIC nanopore protocol for nCoV2019 novel coronavirus
connor-lab/ncov2019-artic-nf
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
nextstrain/ncov
Nextstrain build for novel coronavirus SARS-CoV-2
marbl/canu
A single molecule sequence assembler for genomes large and small.
matted-zz/genome_coverage_plotter
Simple script to generate whole-genome coverage plots
tseemann/abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
OpenGene/fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
aldertzomer/RFPlasmid
Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf
aldertzomer/cgmlst
Fork of mlst of tseemann modified for cgmlst. Not very fast when used with organisms with a large number of allelic variants
aldertzomer/FastDeMe
A fast, easy solution for metagenomic data analysis - Forked from Sander Vermeulens repository, developed during his internship
quinlan-lab/applied-computational-genomics
Applied Computational Genomics Course at UU: Spring 2020
BenLangmead/bowtie2
A fast and sensitive gapped read aligner
nickjcroucher/gubbins
Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins
thlee/SNPhylo
A pipeline to generate a phylogenetic tree from huge SNP data
sanger-pathogens/snp-sites
Finds SNP sites from a multi-FASTA alignment file
sanger-pathogens/Roary
Rapid large-scale prokaryote pan genome analysis
AdmiralenOla/Scoary
Pan-genome wide association studies
YuLab-SMU/ggtree
:christmas_tree:Visualization and annotation of phylogenetic trees
linnabrown/run_dbcan
Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
yaricom/english-article-correction
The experiment with applying NLP to correction of definite/indefinite articles in English text corpus
chrisjbryant/lmgec-lite
A language model-based approach to Grammatical Error Correction for English that uses minimal annotated data.
electron-userland/electron-spellchecker
Implement spellchecking, correctly