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abricate

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

alcov

alphafold

Open source code for AlphaFold.

autoviz

Automatically Visualize any dataset, any size with a single line of code. Created by Ram Seshadri. Collaborators Welcome. Permission Granted upon Request.

awesome-bioinformatics

A curated list of awesome Bioinformatics libraries and software.

bactdating

Bayesian inference of ancestral dates on bacterial phylogenetic trees

bactmap

A mapping-based pipeline for creating a phylogeny from bacterial whole genome sequences

bactopia

A flexible pipeline for complete analysis of bacterial genomes

bactspeciesid

Fast microbial species identification (16S rRNA gene-based approach) and contamination check using whole genome assemblies

bam-readcount

count DNA sequence reads in BAM files

bamsurgeon

tools for adding mutations to existing .bam files, used for testing mutation callers

biobakery

bioBakery tools for meta'omic profiling

biocode

Bioinformatics code libraries and scripts

bioinformatics-one-liners

Bioinformatics one liners from Ming Tang

biotools

A list of useful bioinformatics resources

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

cheatsheets

RStudio Cheat Sheets

clinker

Gene cluster comparison figure generator

cojac

covizu

Rapid analysis and visualization of coronavirus genome variation

crisprcasfinder

A Perl script allowing to identify CRISPR arrays and associated Cas proteins from DNA sequences

crisprcastyper

CCTyper: Automatic detection and subtyping of CRISPR-Cas operons

d3-graph-gallery

A collection of simple graphics made with D3.js

deepbgc

BGC Detection and Classification Using Deep Learning

dgl-lifesci

Python package for graph neural networks in chemistry and biology

dram

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

easyfig

Development version of Easyfig

fastqcheck

Generate statistics on and validate fastq files

freyja

Depth-weighted De-Mixing

gggenomes

A grammar of graphics for comparative genomics