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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

beav

BEAV: Bacterial Element Annotation reVamped

bigsdb

Bacterial Isolate Genome Sequence Database (BIGSdb): A platform for gene-by-gene bacterial population annotation and analysis.

bincrisp

Find CRISPRS in genomes using pilercr & draws a matrix

bioinformaticspracticals

Practical Introduction to Bioinformatics and Systems Biology with R (mainly)

bonito

A PyTorch Basecaller for Oxford Nanopore Reads

bowtie2

A fast and sensitive gapped read aligner

brig

BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.

canu

A single molecule sequence assembler for genomes large and small.

clonalorigin

Inference of homologous recombination in bacteria using whole genome sequences

comparative_genomics_of_virulence_factors

In this repository, you will find some scripts and commands to perform specific comparative genomics analysis

csesa

:exclamation: This is a read-only mirror of the CRAN R package repository. CSESA — CRISPR-Based Salmonella Enterica Serotype Analyzer

deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads

deepsignalingpathwayprediction

Pathway prediction methylation

degenprimer

DegenPrimer is a tool to check the quality of degenerate primers by simulating PCR

degeprime

A program for degenerate primer design for broad taxonomic-range PCR for microbial ecology studies

deltarpkm

An R package for a rapid differential gene presence analysis between similar genomes

dragonflye

:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads

epi-gene

flye

De novo assembler for single molecule sequencing reads using repeat graphs

gaap-bp

Genome Assembly and Annotation Pipeline for Bacteria Pacbio

genemates

An R package identifying horizontal gene co-transfer between bacteria using association analysis and whole-genome sequences