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