Pinned Repositories
2017-ucsc-metagenomics
Workshop materials for shotgun metagenomics
abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
acPCoA
Adjustment for Confounding Factors using Principal Coordinate Analysis
AMR-meta
kmer- and matrix-factorization-based classifier for metagenomics data
ANT
Ambiguous Nucleotide Tool (ANT), software for generating and evaluating degenerate codons for natural and expanded genetic codes.
awesome-R
A curated list of awesome R packages, frameworks and software.
bac-genomics-scripts
Collection of scripts for bacterial genomics
bactmap
A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences
bakta
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
Integron_Finder
Bioinformatics tool to find integrons in bacterial genomes
KFWins2022's Repositories
KFWins2022/abricate
:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes
KFWins2022/AMR-meta
kmer- and matrix-factorization-based classifier for metagenomics data
KFWins2022/awesome-R
A curated list of awesome R packages, frameworks and software.
KFWins2022/bakta
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
KFWins2022/Integron_Finder
Bioinformatics tool to find integrons in bacterial genomes
KFWins2022/beav
BEAV: Bacterial Element Annotation reVamped
KFWins2022/BIGSdb
Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.
KFWins2022/bowtie2
A fast and sensitive gapped read aligner
KFWins2022/dragonflye
:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads
KFWins2022/Flye
De novo assembler for single molecule sequencing reads using repeat graphs
KFWins2022/GAAP-BP
Genome Assembly and Annotation Pipeline for Bacteria Pacbio
KFWins2022/gnomeR
Package to wrangle and visualize genomic data in R
KFWins2022/heatmaply
Interactive Heat Maps for R Using plotly
KFWins2022/KFWins2022
Config files for my GitHub profile.
KFWins2022/Lociq
KFWins2022/mob-suite
MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies
KFWins2022/NanoPlot
Plotting scripts for long read sequencing data
KFWins2022/NanoR
Nanopore data analysis in R
KFWins2022/ONN4ARG
ONN4ARG is an ontology-aware neural network model, which employs a novel ontology-aware layer for antibiotic resistance gene prediction and classification.
KFWins2022/Perfect-bacterial-genome-tutorial
KFWins2022/plotgardener
KFWins2022/Polypolish
a short-read polishing tool for long-read assemblies
KFWins2022/Prodigal
Prodigal Gene Prediction Software
KFWins2022/quast
Genome assembly evaluation tool
KFWins2022/shovill
⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads
KFWins2022/SibeliaZ
A fast whole-genome aligner based on de Bruijn graphs
KFWins2022/spades
SPAdes Genome Assembler
KFWins2022/staramr
Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
KFWins2022/Trycycler
A tool for generating consensus long-read assemblies for bacterial genomes
KFWins2022/Unicycler
hybrid assembly pipeline for bacterial genomes